python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL341_b21_RNA_kidneyreredo.T373_b21_Kidney_PCW15.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL341_b21_RNA_kidneyreredo.T373_b21_Kidney_PCW15 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL342_b21_RNA_kidneyreredo.T373_b21_Kidney_PCW15.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL342_b21_RNA_kidneyreredo.T373_b21_Kidney_PCW15 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL341_b21_RNA_kidneyreredo.T397_b21_Kidney_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL341_b21_RNA_kidneyreredo.T397_b21_Kidney_PCW17 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL342_b21_RNA_kidneyreredo.T397_b21_Kidney_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL342_b21_RNA_kidneyreredo.T397_b21_Kidney_PCW17 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL341_b21_RNA_kidneyreredo.T42_b21_Kidney_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL341_b21_RNA_kidneyreredo.T42_b21_Kidney_PCW17 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL342_b21_RNA_kidneyreredo.T42_b21_Kidney_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL342_b21_RNA_kidneyreredo.T42_b21_Kidney_PCW17 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL341_b21_RNA_kidneyreredo.T228_b21_Kidney_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL341_b21_RNA_kidneyreredo.T228_b21_Kidney_PCW21 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL342_b21_RNA_kidneyreredo.T228_b21_Kidney_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL342_b21_RNA_kidneyreredo.T228_b21_Kidney_PCW21 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL341_b21_RNA_kidneyreredo.T271_b21_Kidney_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL341_b21_RNA_kidneyreredo.T271_b21_Kidney_PCW18 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL342_b21_RNA_kidneyreredo.T271_b21_Kidney_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL342_b21_RNA_kidneyreredo.T271_b21_Kidney_PCW18 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL341_b21_RNA_kidneyreredo.T108_b21_Kidney_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL341_b21_RNA_kidneyreredo.T108_b21_Kidney_PCW17 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL342_b21_RNA_kidneyreredo.T108_b21_Kidney_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL342_b21_RNA_kidneyreredo.T108_b21_Kidney_PCW17 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL277_b10_RNA_StomachEsophagus.T238_b10_Stomach_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL277_b10_RNA_StomachEsophagus.T238_b10_Stomach_PCW21 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL278_b10_RNA_StomachEsophagus.T238_b10_Stomach_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL278_b10_RNA_StomachEsophagus.T238_b10_Stomach_PCW21 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL279_b10_RNA_StomachEsophagus.T238_b10_Stomach_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL279_b10_RNA_StomachEsophagus.T238_b10_Stomach_PCW21 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL280_b10_RNA_StomachEsophagus.T238_b10_Stomach_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL280_b10_RNA_StomachEsophagus.T238_b10_Stomach_PCW21 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL277_b10_RNA_StomachEsophagus.T269_b10_Stomach_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL277_b10_RNA_StomachEsophagus.T269_b10_Stomach_PCW18 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL278_b10_RNA_StomachEsophagus.T269_b10_Stomach_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL278_b10_RNA_StomachEsophagus.T269_b10_Stomach_PCW18 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL279_b10_RNA_StomachEsophagus.T269_b10_Stomach_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL279_b10_RNA_StomachEsophagus.T269_b10_Stomach_PCW18 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL280_b10_RNA_StomachEsophagus.T269_b10_Stomach_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL280_b10_RNA_StomachEsophagus.T269_b10_Stomach_PCW18 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL277_b10_RNA_StomachEsophagus.T303_b10_Esophagus_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL277_b10_RNA_StomachEsophagus.T303_b10_Esophagus_PCW21 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL278_b10_RNA_StomachEsophagus.T303_b10_Esophagus_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL278_b10_RNA_StomachEsophagus.T303_b10_Esophagus_PCW21 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL279_b10_RNA_StomachEsophagus.T303_b10_Esophagus_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL279_b10_RNA_StomachEsophagus.T303_b10_Esophagus_PCW21 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL280_b10_RNA_StomachEsophagus.T303_b10_Esophagus_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL280_b10_RNA_StomachEsophagus.T303_b10_Esophagus_PCW21 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL277_b10_RNA_StomachEsophagus.T322_b10_Stomach_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL277_b10_RNA_StomachEsophagus.T322_b10_Stomach_PCW21 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL278_b10_RNA_StomachEsophagus.T322_b10_Stomach_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL278_b10_RNA_StomachEsophagus.T322_b10_Stomach_PCW21 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL279_b10_RNA_StomachEsophagus.T322_b10_Stomach_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL279_b10_RNA_StomachEsophagus.T322_b10_Stomach_PCW21 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL280_b10_RNA_StomachEsophagus.T322_b10_Stomach_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL280_b10_RNA_StomachEsophagus.T322_b10_Stomach_PCW21 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL277_b10_RNA_StomachEsophagus.T35_b10_Stomach_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL277_b10_RNA_StomachEsophagus.T35_b10_Stomach_PCW17 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL278_b10_RNA_StomachEsophagus.T35_b10_Stomach_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL278_b10_RNA_StomachEsophagus.T35_b10_Stomach_PCW17 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL279_b10_RNA_StomachEsophagus.T35_b10_Stomach_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL279_b10_RNA_StomachEsophagus.T35_b10_Stomach_PCW17 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL280_b10_RNA_StomachEsophagus.T35_b10_Stomach_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL280_b10_RNA_StomachEsophagus.T35_b10_Stomach_PCW17 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL277_b10_RNA_StomachEsophagus.T399_b10_Stomach_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL277_b10_RNA_StomachEsophagus.T399_b10_Stomach_PCW17 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL278_b10_RNA_StomachEsophagus.T399_b10_Stomach_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL278_b10_RNA_StomachEsophagus.T399_b10_Stomach_PCW17 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL279_b10_RNA_StomachEsophagus.T399_b10_Stomach_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL279_b10_RNA_StomachEsophagus.T399_b10_Stomach_PCW17 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL280_b10_RNA_StomachEsophagus.T399_b10_Stomach_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL280_b10_RNA_StomachEsophagus.T399_b10_Stomach_PCW17 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL277_b10_RNA_StomachEsophagus.T53_b10_Stomach_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL277_b10_RNA_StomachEsophagus.T53_b10_Stomach_PCW20 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL278_b10_RNA_StomachEsophagus.T53_b10_Stomach_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL278_b10_RNA_StomachEsophagus.T53_b10_Stomach_PCW20 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL279_b10_RNA_StomachEsophagus.T53_b10_Stomach_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL279_b10_RNA_StomachEsophagus.T53_b10_Stomach_PCW20 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL280_b10_RNA_StomachEsophagus.T53_b10_Stomach_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL280_b10_RNA_StomachEsophagus.T53_b10_Stomach_PCW20 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL341_b21_RNA_kidneyreredo.T373_b21_Kidney_PCW15.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL341_b21_RNA_kidneyreredo.T373_b21_Kidney_PCW15 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL342_b21_RNA_kidneyreredo.T373_b21_Kidney_PCW15.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL342_b21_RNA_kidneyreredo.T373_b21_Kidney_PCW15 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL341_b21_RNA_kidneyreredo.T397_b21_Kidney_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL341_b21_RNA_kidneyreredo.T397_b21_Kidney_PCW17 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL342_b21_RNA_kidneyreredo.T397_b21_Kidney_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL342_b21_RNA_kidneyreredo.T397_b21_Kidney_PCW17 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL341_b21_RNA_kidneyreredo.T42_b21_Kidney_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL341_b21_RNA_kidneyreredo.T42_b21_Kidney_PCW17 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL342_b21_RNA_kidneyreredo.T42_b21_Kidney_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL342_b21_RNA_kidneyreredo.T42_b21_Kidney_PCW17 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL341_b21_RNA_kidneyreredo.T228_b21_Kidney_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL341_b21_RNA_kidneyreredo.T228_b21_Kidney_PCW21 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL342_b21_RNA_kidneyreredo.T228_b21_Kidney_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL342_b21_RNA_kidneyreredo.T228_b21_Kidney_PCW21 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL341_b21_RNA_kidneyreredo.T271_b21_Kidney_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL341_b21_RNA_kidneyreredo.T271_b21_Kidney_PCW18 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL342_b21_RNA_kidneyreredo.T271_b21_Kidney_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL342_b21_RNA_kidneyreredo.T271_b21_Kidney_PCW18 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL341_b21_RNA_kidneyreredo.T108_b21_Kidney_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL341_b21_RNA_kidneyreredo.T108_b21_Kidney_PCW17 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL342_b21_RNA_kidneyreredo.T108_b21_Kidney_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL342_b21_RNA_kidneyreredo.T108_b21_Kidney_PCW17 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL277_b10_RNA_StomachEsophagus.T238_b10_Stomach_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL277_b10_RNA_StomachEsophagus.T238_b10_Stomach_PCW21 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL278_b10_RNA_StomachEsophagus.T238_b10_Stomach_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL278_b10_RNA_StomachEsophagus.T238_b10_Stomach_PCW21 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL279_b10_RNA_StomachEsophagus.T238_b10_Stomach_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL279_b10_RNA_StomachEsophagus.T238_b10_Stomach_PCW21 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL280_b10_RNA_StomachEsophagus.T238_b10_Stomach_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL280_b10_RNA_StomachEsophagus.T238_b10_Stomach_PCW21 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL277_b10_RNA_StomachEsophagus.T269_b10_Stomach_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL277_b10_RNA_StomachEsophagus.T269_b10_Stomach_PCW18 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL278_b10_RNA_StomachEsophagus.T269_b10_Stomach_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL278_b10_RNA_StomachEsophagus.T269_b10_Stomach_PCW18 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL279_b10_RNA_StomachEsophagus.T269_b10_Stomach_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL279_b10_RNA_StomachEsophagus.T269_b10_Stomach_PCW18 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL280_b10_RNA_StomachEsophagus.T269_b10_Stomach_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL280_b10_RNA_StomachEsophagus.T269_b10_Stomach_PCW18 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL277_b10_RNA_StomachEsophagus.T303_b10_Esophagus_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL277_b10_RNA_StomachEsophagus.T303_b10_Esophagus_PCW21 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL278_b10_RNA_StomachEsophagus.T303_b10_Esophagus_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL278_b10_RNA_StomachEsophagus.T303_b10_Esophagus_PCW21 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL279_b10_RNA_StomachEsophagus.T303_b10_Esophagus_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL279_b10_RNA_StomachEsophagus.T303_b10_Esophagus_PCW21 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL280_b10_RNA_StomachEsophagus.T303_b10_Esophagus_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL280_b10_RNA_StomachEsophagus.T303_b10_Esophagus_PCW21 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL277_b10_RNA_StomachEsophagus.T322_b10_Stomach_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL277_b10_RNA_StomachEsophagus.T322_b10_Stomach_PCW21 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL278_b10_RNA_StomachEsophagus.T322_b10_Stomach_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL278_b10_RNA_StomachEsophagus.T322_b10_Stomach_PCW21 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL279_b10_RNA_StomachEsophagus.T322_b10_Stomach_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL279_b10_RNA_StomachEsophagus.T322_b10_Stomach_PCW21 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL280_b10_RNA_StomachEsophagus.T322_b10_Stomach_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL280_b10_RNA_StomachEsophagus.T322_b10_Stomach_PCW21 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL277_b10_RNA_StomachEsophagus.T35_b10_Stomach_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL277_b10_RNA_StomachEsophagus.T35_b10_Stomach_PCW17 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL278_b10_RNA_StomachEsophagus.T35_b10_Stomach_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL278_b10_RNA_StomachEsophagus.T35_b10_Stomach_PCW17 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL279_b10_RNA_StomachEsophagus.T35_b10_Stomach_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL279_b10_RNA_StomachEsophagus.T35_b10_Stomach_PCW17 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL280_b10_RNA_StomachEsophagus.T35_b10_Stomach_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL280_b10_RNA_StomachEsophagus.T35_b10_Stomach_PCW17 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL277_b10_RNA_StomachEsophagus.T399_b10_Stomach_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL277_b10_RNA_StomachEsophagus.T399_b10_Stomach_PCW17 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL278_b10_RNA_StomachEsophagus.T399_b10_Stomach_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL278_b10_RNA_StomachEsophagus.T399_b10_Stomach_PCW17 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL279_b10_RNA_StomachEsophagus.T399_b10_Stomach_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL279_b10_RNA_StomachEsophagus.T399_b10_Stomach_PCW17 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL280_b10_RNA_StomachEsophagus.T399_b10_Stomach_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL280_b10_RNA_StomachEsophagus.T399_b10_Stomach_PCW17 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL277_b10_RNA_StomachEsophagus.T53_b10_Stomach_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL277_b10_RNA_StomachEsophagus.T53_b10_Stomach_PCW20 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL278_b10_RNA_StomachEsophagus.T53_b10_Stomach_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL278_b10_RNA_StomachEsophagus.T53_b10_Stomach_PCW20 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL279_b10_RNA_StomachEsophagus.T53_b10_Stomach_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL279_b10_RNA_StomachEsophagus.T53_b10_Stomach_PCW20 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL280_b10_RNA_StomachEsophagus.T53_b10_Stomach_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL280_b10_RNA_StomachEsophagus.T53_b10_Stomach_PCW20 -nomulti &