python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL20_b1_RNA_lung.T_107_b1_Lung_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL20_b1_RNA_lung.T_107_b1_Lung_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 SL20_b1_RNA_lung.T_157_b1_Lung_PCW10.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL20_b1_RNA_lung.T_157_b1_Lung_PCW10 -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 SL20_b1_RNA_lung.T_226_b1_Lung_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL20_b1_RNA_lung.T_226_b1_Lung_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 SL20_b1_RNA_lung.T_256_b1_Lung_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL20_b1_RNA_lung.T_256_b1_Lung_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 SL20_b1_RNA_lung.T_286_b1_Lung_PCW14.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL20_b1_RNA_lung.T_286_b1_Lung_PCW14 -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 SL20_b1_RNA_lung.T_304_b1_Lung_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL20_b1_RNA_lung.T_304_b1_Lung_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 SL20_b1_RNA_lung.T_381_b1_Lung_PCW15.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL20_b1_RNA_lung.T_381_b1_Lung_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 SL20_b1_RNA_lung.T_408L_b1_Lung_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL20_b1_RNA_lung.T_408L_b1_Lung_PCW19 -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 SL24_b1_RNA_lung.T_107_b1_Lung_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL24_b1_RNA_lung.T_107_b1_Lung_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 SL24_b1_RNA_lung.T_157_b1_Lung_PCW10.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL24_b1_RNA_lung.T_157_b1_Lung_PCW10 -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 SL24_b1_RNA_lung.T_226_b1_Lung_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL24_b1_RNA_lung.T_226_b1_Lung_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 SL24_b1_RNA_lung.T_256_b1_Lung_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL24_b1_RNA_lung.T_256_b1_Lung_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 SL24_b1_RNA_lung.T_286_b1_Lung_PCW14.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL24_b1_RNA_lung.T_286_b1_Lung_PCW14 -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 SL24_b1_RNA_lung.T_304_b1_Lung_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL24_b1_RNA_lung.T_304_b1_Lung_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 SL24_b1_RNA_lung.T_381_b1_Lung_PCW15.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL24_b1_RNA_lung.T_381_b1_Lung_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 SL24_b1_RNA_lung.T_408L_b1_Lung_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL24_b1_RNA_lung.T_408L_b1_Lung_PCW19 -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 SL25_b2_RNA_lung.T_125_b2_Lung_PCW22.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL25_b2_RNA_lung.T_125_b2_Lung_PCW22 -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 SL25_b2_RNA_lung.T_174_b2_Lung_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL25_b2_RNA_lung.T_174_b2_Lung_PCW19 -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 SL25_b2_RNA_lung.T_198_b2_Lung_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL25_b2_RNA_lung.T_198_b2_Lung_PCW23 -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 SL25_b2_RNA_lung.T_24_b2_Lung_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL25_b2_RNA_lung.T_24_b2_Lung_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 SL25_b2_RNA_lung.T_304_b2_Lung_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL25_b2_RNA_lung.T_304_b2_Lung_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 SL25_b2_RNA_lung.T_333_b2_Lung_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL25_b2_RNA_lung.T_333_b2_Lung_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 SL25_b2_RNA_lung.T_49_b2_Lung_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL25_b2_RNA_lung.T_49_b2_Lung_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 SL25_b2_RNA_lung.T_77_b2_Lung_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL25_b2_RNA_lung.T_77_b2_Lung_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 SL32_b2_RNA_lung.T_125_b2_Lung_PCW22.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL32_b2_RNA_lung.T_125_b2_Lung_PCW22 -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 SL32_b2_RNA_lung.T_174_b2_Lung_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL32_b2_RNA_lung.T_174_b2_Lung_PCW19 -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 SL32_b2_RNA_lung.T_198_b2_Lung_PCW23.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL32_b2_RNA_lung.T_198_b2_Lung_PCW23 -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 SL32_b2_RNA_lung.T_24_b2_Lung_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL32_b2_RNA_lung.T_24_b2_Lung_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 SL32_b2_RNA_lung.T_304_b2_Lung_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL32_b2_RNA_lung.T_304_b2_Lung_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 SL32_b2_RNA_lung.T_333_b2_Lung_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL32_b2_RNA_lung.T_333_b2_Lung_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 SL32_b2_RNA_lung.T_49_b2_Lung_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL32_b2_RNA_lung.T_49_b2_Lung_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 SL32_b2_RNA_lung.T_77_b2_Lung_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL32_b2_RNA_lung.T_77_b2_Lung_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 SL51_b3_RNA_kidney.T108_b3_Kidney_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL51_b3_RNA_kidney.T108_b3_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 SL51_b3_RNA_kidney.T181_b3_Kidney_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL51_b3_RNA_kidney.T181_b3_Kidney_PCW19 -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 SL51_b3_RNA_kidney.T284_b3_Kidney_PCW14.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL51_b3_RNA_kidney.T284_b3_Kidney_PCW14 -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 SL51_b3_RNA_kidney.T309_b3_Kidney_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL51_b3_RNA_kidney.T309_b3_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 SL51_b3_RNA_kidney.T359_b3_Kidney_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL51_b3_RNA_kidney.T359_b3_Kidney_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 SL51_b3_RNA_kidney.T373_b3_Kidney_PCW15.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL51_b3_RNA_kidney.T373_b3_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 SL51_b3_RNA_kidney.T389_b3_Kidney_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL51_b3_RNA_kidney.T389_b3_Kidney_PCW13 -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 SL51_b3_RNA_kidney.T65_b3_Kidney_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL51_b3_RNA_kidney.T65_b3_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 SL53_b3_RNA_kidney.T108_b3_Kidney_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL53_b3_RNA_kidney.T108_b3_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 SL53_b3_RNA_kidney.T181_b3_Kidney_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL53_b3_RNA_kidney.T181_b3_Kidney_PCW19 -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 SL53_b3_RNA_kidney.T284_b3_Kidney_PCW14.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL53_b3_RNA_kidney.T284_b3_Kidney_PCW14 -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 SL53_b3_RNA_kidney.T309_b3_Kidney_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL53_b3_RNA_kidney.T309_b3_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 SL53_b3_RNA_kidney.T359_b3_Kidney_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL53_b3_RNA_kidney.T359_b3_Kidney_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 SL53_b3_RNA_kidney.T373_b3_Kidney_PCW15.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL53_b3_RNA_kidney.T373_b3_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 SL53_b3_RNA_kidney.T389_b3_Kidney_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL53_b3_RNA_kidney.T389_b3_Kidney_PCW13 -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 SL53_b3_RNA_kidney.T65_b3_Kidney_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL53_b3_RNA_kidney.T65_b3_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 SL58_b4_RNA_brain.T129_b4_Brain_PCW22.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL58_b4_RNA_brain.T129_b4_Brain_PCW22 -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 SL58_b4_RNA_brain.T155_b4_Brain_PCW10.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL58_b4_RNA_brain.T155_b4_Brain_PCW10 -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 SL58_b4_RNA_brain.T183_b4_Brain_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL58_b4_RNA_brain.T183_b4_Brain_PCW19 -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 SL58_b4_RNA_brain.T382_b4_Brain_PCW15.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL58_b4_RNA_brain.T382_b4_Brain_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 SL58_b4_RNA_brain.T47_b4_Brain_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL58_b4_RNA_brain.T47_b4_Brain_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 SL58_b4_RNA_brain.T63_b4_Brain_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL58_b4_RNA_brain.T63_b4_Brain_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 SL58_b4_RNA_brain.T64_b4_Brain_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL58_b4_RNA_brain.T64_b4_Brain_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 SL58_b4_RNA_brain.T94_b4_Brain_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL58_b4_RNA_brain.T94_b4_Brain_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 SL63_b4_RNA_brain.T129_b4_Brain_PCW22.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL63_b4_RNA_brain.T129_b4_Brain_PCW22 -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 SL63_b4_RNA_brain.T155_b4_Brain_PCW10.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL63_b4_RNA_brain.T155_b4_Brain_PCW10 -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 SL63_b4_RNA_brain.T183_b4_Brain_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL63_b4_RNA_brain.T183_b4_Brain_PCW19 -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 SL63_b4_RNA_brain.T382_b4_Brain_PCW15.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL63_b4_RNA_brain.T382_b4_Brain_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 SL63_b4_RNA_brain.T47_b4_Brain_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL63_b4_RNA_brain.T47_b4_Brain_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 SL63_b4_RNA_brain.T63_b4_Brain_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL63_b4_RNA_brain.T63_b4_Brain_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 SL63_b4_RNA_brain.T64_b4_Brain_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL63_b4_RNA_brain.T64_b4_Brain_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 SL63_b4_RNA_brain.T94_b4_Brain_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL63_b4_RNA_brain.T94_b4_Brain_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/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL20_b1_RNA_lung.T_107_b1_Lung_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-SL20_b1_RNA_lung.T_107_b1_Lung_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 SL20_b1_RNA_lung.T_157_b1_Lung_PCW10.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-SL20_b1_RNA_lung.T_157_b1_Lung_PCW10 -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 SL20_b1_RNA_lung.T_226_b1_Lung_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-SL20_b1_RNA_lung.T_226_b1_Lung_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 SL20_b1_RNA_lung.T_256_b1_Lung_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-SL20_b1_RNA_lung.T_256_b1_Lung_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 SL20_b1_RNA_lung.T_286_b1_Lung_PCW14.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-SL20_b1_RNA_lung.T_286_b1_Lung_PCW14 -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 SL20_b1_RNA_lung.T_304_b1_Lung_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-SL20_b1_RNA_lung.T_304_b1_Lung_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 SL20_b1_RNA_lung.T_381_b1_Lung_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-SL20_b1_RNA_lung.T_381_b1_Lung_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 SL20_b1_RNA_lung.T_408L_b1_Lung_PCW19.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-SL20_b1_RNA_lung.T_408L_b1_Lung_PCW19 -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 SL24_b1_RNA_lung.T_107_b1_Lung_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-SL24_b1_RNA_lung.T_107_b1_Lung_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 SL24_b1_RNA_lung.T_157_b1_Lung_PCW10.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-SL24_b1_RNA_lung.T_157_b1_Lung_PCW10 -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 SL24_b1_RNA_lung.T_226_b1_Lung_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-SL24_b1_RNA_lung.T_226_b1_Lung_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 SL24_b1_RNA_lung.T_256_b1_Lung_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-SL24_b1_RNA_lung.T_256_b1_Lung_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 SL24_b1_RNA_lung.T_286_b1_Lung_PCW14.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-SL24_b1_RNA_lung.T_286_b1_Lung_PCW14 -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 SL24_b1_RNA_lung.T_304_b1_Lung_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-SL24_b1_RNA_lung.T_304_b1_Lung_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 SL24_b1_RNA_lung.T_381_b1_Lung_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-SL24_b1_RNA_lung.T_381_b1_Lung_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 SL24_b1_RNA_lung.T_408L_b1_Lung_PCW19.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-SL24_b1_RNA_lung.T_408L_b1_Lung_PCW19 -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 SL25_b2_RNA_lung.T_125_b2_Lung_PCW22.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-SL25_b2_RNA_lung.T_125_b2_Lung_PCW22 -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 SL25_b2_RNA_lung.T_174_b2_Lung_PCW19.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-SL25_b2_RNA_lung.T_174_b2_Lung_PCW19 -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 SL25_b2_RNA_lung.T_198_b2_Lung_PCW23.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-SL25_b2_RNA_lung.T_198_b2_Lung_PCW23 -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 SL25_b2_RNA_lung.T_24_b2_Lung_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-SL25_b2_RNA_lung.T_24_b2_Lung_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 SL25_b2_RNA_lung.T_304_b2_Lung_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-SL25_b2_RNA_lung.T_304_b2_Lung_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 SL25_b2_RNA_lung.T_333_b2_Lung_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-SL25_b2_RNA_lung.T_333_b2_Lung_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 SL25_b2_RNA_lung.T_49_b2_Lung_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-SL25_b2_RNA_lung.T_49_b2_Lung_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 SL25_b2_RNA_lung.T_77_b2_Lung_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-SL25_b2_RNA_lung.T_77_b2_Lung_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 SL32_b2_RNA_lung.T_125_b2_Lung_PCW22.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-SL32_b2_RNA_lung.T_125_b2_Lung_PCW22 -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 SL32_b2_RNA_lung.T_174_b2_Lung_PCW19.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-SL32_b2_RNA_lung.T_174_b2_Lung_PCW19 -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 SL32_b2_RNA_lung.T_198_b2_Lung_PCW23.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-SL32_b2_RNA_lung.T_198_b2_Lung_PCW23 -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 SL32_b2_RNA_lung.T_24_b2_Lung_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-SL32_b2_RNA_lung.T_24_b2_Lung_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 SL32_b2_RNA_lung.T_304_b2_Lung_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-SL32_b2_RNA_lung.T_304_b2_Lung_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 SL32_b2_RNA_lung.T_333_b2_Lung_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-SL32_b2_RNA_lung.T_333_b2_Lung_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 SL32_b2_RNA_lung.T_49_b2_Lung_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-SL32_b2_RNA_lung.T_49_b2_Lung_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 SL32_b2_RNA_lung.T_77_b2_Lung_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-SL32_b2_RNA_lung.T_77_b2_Lung_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 SL51_b3_RNA_kidney.T108_b3_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-SL51_b3_RNA_kidney.T108_b3_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 SL51_b3_RNA_kidney.T181_b3_Kidney_PCW19.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-SL51_b3_RNA_kidney.T181_b3_Kidney_PCW19 -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 SL51_b3_RNA_kidney.T284_b3_Kidney_PCW14.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-SL51_b3_RNA_kidney.T284_b3_Kidney_PCW14 -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 SL51_b3_RNA_kidney.T309_b3_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-SL51_b3_RNA_kidney.T309_b3_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 SL51_b3_RNA_kidney.T359_b3_Kidney_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-SL51_b3_RNA_kidney.T359_b3_Kidney_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 SL51_b3_RNA_kidney.T373_b3_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-SL51_b3_RNA_kidney.T373_b3_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 SL51_b3_RNA_kidney.T389_b3_Kidney_PCW13.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-SL51_b3_RNA_kidney.T389_b3_Kidney_PCW13 -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 SL51_b3_RNA_kidney.T65_b3_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-SL51_b3_RNA_kidney.T65_b3_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 SL53_b3_RNA_kidney.T108_b3_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-SL53_b3_RNA_kidney.T108_b3_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 SL53_b3_RNA_kidney.T181_b3_Kidney_PCW19.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-SL53_b3_RNA_kidney.T181_b3_Kidney_PCW19 -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 SL53_b3_RNA_kidney.T284_b3_Kidney_PCW14.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-SL53_b3_RNA_kidney.T284_b3_Kidney_PCW14 -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 SL53_b3_RNA_kidney.T309_b3_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-SL53_b3_RNA_kidney.T309_b3_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 SL53_b3_RNA_kidney.T359_b3_Kidney_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-SL53_b3_RNA_kidney.T359_b3_Kidney_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 SL53_b3_RNA_kidney.T373_b3_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-SL53_b3_RNA_kidney.T373_b3_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 SL53_b3_RNA_kidney.T389_b3_Kidney_PCW13.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-SL53_b3_RNA_kidney.T389_b3_Kidney_PCW13 -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 SL53_b3_RNA_kidney.T65_b3_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-SL53_b3_RNA_kidney.T65_b3_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 SL58_b4_RNA_brain.T129_b4_Brain_PCW22.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-SL58_b4_RNA_brain.T129_b4_Brain_PCW22 -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 SL58_b4_RNA_brain.T155_b4_Brain_PCW10.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-SL58_b4_RNA_brain.T155_b4_Brain_PCW10 -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 SL58_b4_RNA_brain.T183_b4_Brain_PCW19.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-SL58_b4_RNA_brain.T183_b4_Brain_PCW19 -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 SL58_b4_RNA_brain.T382_b4_Brain_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-SL58_b4_RNA_brain.T382_b4_Brain_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 SL58_b4_RNA_brain.T47_b4_Brain_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-SL58_b4_RNA_brain.T47_b4_Brain_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 SL58_b4_RNA_brain.T63_b4_Brain_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-SL58_b4_RNA_brain.T63_b4_Brain_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 SL58_b4_RNA_brain.T64_b4_Brain_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-SL58_b4_RNA_brain.T64_b4_Brain_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 SL58_b4_RNA_brain.T94_b4_Brain_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-SL58_b4_RNA_brain.T94_b4_Brain_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 SL63_b4_RNA_brain.T129_b4_Brain_PCW22.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-SL63_b4_RNA_brain.T129_b4_Brain_PCW22 -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 SL63_b4_RNA_brain.T155_b4_Brain_PCW10.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-SL63_b4_RNA_brain.T155_b4_Brain_PCW10 -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 SL63_b4_RNA_brain.T183_b4_Brain_PCW19.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-SL63_b4_RNA_brain.T183_b4_Brain_PCW19 -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 SL63_b4_RNA_brain.T382_b4_Brain_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-SL63_b4_RNA_brain.T382_b4_Brain_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 SL63_b4_RNA_brain.T47_b4_Brain_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-SL63_b4_RNA_brain.T47_b4_Brain_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 SL63_b4_RNA_brain.T63_b4_Brain_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-SL63_b4_RNA_brain.T63_b4_Brain_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 SL63_b4_RNA_brain.T64_b4_Brain_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-SL63_b4_RNA_brain.T64_b4_Brain_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 SL63_b4_RNA_brain.T94_b4_Brain_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-SL63_b4_RNA_brain.T94_b4_Brain_PCW17 -nomulti &