python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL289_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T175_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T24_b18_Lung_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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T175_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T24_b18_Lung_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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL313_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T11_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL313_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T408S_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T11_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL314_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T408S_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL289_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T175_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T24_b18_Lung_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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T175_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T24_b18_Lung_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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL313_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T11_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL313_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T408S_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T11_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL314_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T408S_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL289_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T175_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T24_b18_Lung_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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T175_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T24_b18_Lung_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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL313_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T11_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL313_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T408S_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T11_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL314_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T408S_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL289_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T175_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T24_b18_Lung_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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T175_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T24_b18_Lung_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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL313_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T11_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL313_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T408S_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T11_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL314_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T408S_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL289_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T175_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T24_b18_Lung_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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T175_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T24_b18_Lung_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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL313_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T11_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL313_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T408S_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T11_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL314_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T408S_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL289_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T175_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T24_b18_Lung_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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T175_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T24_b18_Lung_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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL313_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T11_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL313_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T408S_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T11_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL314_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T408S_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL289_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T175_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T24_b18_Lung_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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T175_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T24_b18_Lung_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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL313_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T11_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL313_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T408S_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T11_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL314_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T408S_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL289_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T175_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T24_b18_Lung_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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T175_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T24_b18_Lung_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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL313_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T11_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL313_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T408S_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T11_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL314_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T408S_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL289_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T175_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T24_b18_Lung_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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T175_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T24_b18_Lung_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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL313_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T11_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL313_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T408S_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T11_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL314_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T408S_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL289_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T175_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T24_b18_Lung_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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T175_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T24_b18_Lung_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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL313_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T11_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL313_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T408S_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T11_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL314_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T408S_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL289_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T175_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T24_b18_Lung_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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T175_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T24_b18_Lung_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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL313_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T11_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL313_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T408S_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T11_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL314_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T408S_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL289_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T175_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T24_b18_Lung_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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T175_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T24_b18_Lung_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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL313_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T11_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL313_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T408S_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T11_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL314_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T408S_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL289_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T175_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T24_b18_Lung_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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T175_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T24_b18_Lung_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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL313_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T11_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL313_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T408S_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T11_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL314_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T408S_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL289_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T175_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T24_b18_Lung_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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T175_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T24_b18_Lung_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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL313_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T11_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL313_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T408S_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T11_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL314_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T408S_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL289_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T175_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T24_b18_Lung_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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T175_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T24_b18_Lung_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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL313_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T11_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL313_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T408S_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T11_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL314_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T408S_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL289_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T175_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T24_b18_Lung_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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T175_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T24_b18_Lung_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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL313_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T11_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL313_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T408S_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T11_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL314_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T408S_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL289_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T175_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T24_b18_Lung_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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T175_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T24_b18_Lung_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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL313_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T11_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL313_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T408S_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T11_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL314_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T408S_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL289_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T175_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T24_b18_Lung_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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T175_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T24_b18_Lung_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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL313_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T11_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL313_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T408S_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T11_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL314_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T408S_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL289_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T175_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T24_b18_Lung_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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T175_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T24_b18_Lung_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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL313_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T11_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL313_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T408S_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T11_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL314_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T408S_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL289_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T175_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T24_b18_Lung_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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T175_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T24_b18_Lung_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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL313_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T11_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL313_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T408S_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T11_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL314_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T408S_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL289_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T175_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T24_b18_Lung_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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T175_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T24_b18_Lung_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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL313_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T11_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL313_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T408S_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T11_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL314_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T408S_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL289_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T175_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T24_b18_Lung_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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T175_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T24_b18_Lung_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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL313_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T11_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL313_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T408S_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T11_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL314_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T408S_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL289_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T175_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T24_b18_Lung_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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T175_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T24_b18_Lung_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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL313_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T11_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL313_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T408S_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T11_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL314_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T408S_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL289_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T175_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T24_b18_Lung_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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T175_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T24_b18_Lung_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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL313_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T11_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL313_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T408S_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T11_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL314_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T408S_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL289_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T175_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T198_b18_Lung_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 SL289_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T24_b18_Lung_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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL289_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T49_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL289_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T175_b18_Lung_PCW19.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T175_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T198_b18_Lung_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 SL290_b18_RNA_lungredo2.T24_b18_Lung_PCW17.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T24_b18_Lung_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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T305_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.end1.hg38-STAR-2.5.3a/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 SL290_b18_RNA_lungredo2.T333_b18_Lung_PCW21.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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T49_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL290_b18_RNA_lungredo2.T77_b18_Lung_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 SL313_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T11_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T187_b19_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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL313_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL313_b19_RNA_skinredo.T408S_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL313_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T11_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T11_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T187_b19_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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T299_b19_Scalp_PCW21.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 SL314_b19_RNA_skinredo.T408S_b19_Skin_PCW19.end1.hg38-STAR-2.5.3a/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 SL314_b19_RNA_skinredo.T408S_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL314_b19_RNA_skinredo.T45_b19_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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL321_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL321_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T108_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_PCW19.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T181_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T271_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T309_b20_Kidney_PCW21.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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T359_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T373_b20_Kidney_PCW15.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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_PCW17.end1.hg38-STAR-2.5.3a/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 SL322_b20_RNA_kidneyredo.T42_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_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 SL322_b20_RNA_kidneyredo.T65_b20_Kidney_PCW18.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &