python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_RNA_counts.py SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL245_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL247_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL248_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL249_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL250_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL251_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL252_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/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 SL253_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a.SHARE-seq_RNA_counts.gencode.v26.annotation-chrM -UMIedit 1 &