python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr1 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr1 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr2 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr2 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr3 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr4 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr4 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr5 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr5 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr6 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr6 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr7 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr7 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr8 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr8 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr9 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr9 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr10 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr10 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr11 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr11 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr12 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr12 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr13 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr13 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr14 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr14 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr15 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr15 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr16 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr16 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr17 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr17 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr18 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr18 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr19 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr19 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr20 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr20 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr21 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr21 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chr22 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chr22 -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrX /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrX -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrY /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrY -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T11_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T178_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T187_b14_Skin_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T408S_b14_Skin_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T45_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T60_b14_Skin_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T85_b14_Skin_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL201_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL202_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL203_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL204_b14_RNA_Skin.T109_b14_Skin_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T106_b13_Eye_PCW17.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T180_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T186_b13_Eye_PCW23.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T410_b13_Eye_PCW13.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T51_b13_Eye_PCW20.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T5_b13_Eye_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL194_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL195_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL196_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL197_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL199_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.annotation.gtf.chrM /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes SL200_b13_RNA_EyeRedo.T79_b13_Eye_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &