python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL265_b9_RNA_Muscle.T10_b9_Muscle_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL265_b9_RNA_Muscle.T10_b9_Muscle_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 SL265_b9_RNA_Muscle.T123_b9_Muscle_PCW22.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL265_b9_RNA_Muscle.T123_b9_Muscle_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 SL265_b9_RNA_Muscle.T161_b9_Muscle_PCW10.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL265_b9_RNA_Muscle.T161_b9_Muscle_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 SL265_b9_RNA_Muscle.T377_b9_Muscle_PCW15.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL265_b9_RNA_Muscle.T377_b9_Muscle_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 SL265_b9_RNA_Muscle.T44_b9_Muscle_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL265_b9_RNA_Muscle.T44_b9_Muscle_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 SL265_b9_RNA_Muscle.T61_b9_Muscle_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL265_b9_RNA_Muscle.T61_b9_Muscle_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 SL265_b9_RNA_Muscle.T87_b9_Muscle_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL265_b9_RNA_Muscle.T87_b9_Muscle_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 SL265_b9_RNA_Muscle.T96_b9_Muscle_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL265_b9_RNA_Muscle.T96_b9_Muscle_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 SL254_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL254_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL255_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL255_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL256_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL256_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL257_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL257_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL258_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL258_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL259_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL259_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL260_b17_RNA_SpleenThymus.T165_b17_Spleen_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL260_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL254_b17_RNA_SpleenThymus.T233_b17_Thymus_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL254_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL255_b17_RNA_SpleenThymus.T233_b17_Thymus_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL255_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL256_b17_RNA_SpleenThymus.T233_b17_Thymus_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL256_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL257_b17_RNA_SpleenThymus.T233_b17_Thymus_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL257_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL258_b17_RNA_SpleenThymus.T233_b17_Thymus_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL258_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL259_b17_RNA_SpleenThymus.T233_b17_Thymus_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL259_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL260_b17_RNA_SpleenThymus.T233_b17_Thymus_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL260_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL254_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL254_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL255_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL255_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL256_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL256_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL257_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL257_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL258_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL258_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL259_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL259_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL260_b17_RNA_SpleenThymus.T23_b17_Thymus_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL260_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL254_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL254_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL255_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL255_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL256_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL256_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL257_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL257_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL258_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL258_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL259_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL259_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL260_b17_RNA_SpleenThymus.T270_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL260_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL254_b17_RNA_SpleenThymus.T314_b17_Spleen_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL254_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL255_b17_RNA_SpleenThymus.T314_b17_Spleen_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL255_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL256_b17_RNA_SpleenThymus.T314_b17_Spleen_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL256_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL257_b17_RNA_SpleenThymus.T314_b17_Spleen_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL257_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL258_b17_RNA_SpleenThymus.T314_b17_Spleen_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL258_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL259_b17_RNA_SpleenThymus.T314_b17_Spleen_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL259_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL260_b17_RNA_SpleenThymus.T314_b17_Spleen_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL260_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL254_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL254_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL255_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL255_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL256_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL256_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL257_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL257_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL258_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL258_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL259_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL259_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL260_b17_RNA_SpleenThymus.T406_b17_Thymus_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL260_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL254_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL254_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL255_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL255_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL256_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL256_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL257_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL257_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL258_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL258_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL259_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL259_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL260_b17_RNA_SpleenThymus.T88_b17_Spleen_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL260_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL254_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL254_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL255_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL255_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL256_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL256_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL257_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL257_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL258_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL258_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL259_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL259_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL260_b17_RNA_SpleenThymus.T90_b17_Thymus_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL260_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL263_b15_RNA_AdrenalThyroidSpleen.T136_b16_Thyroid_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL263_b15_RNA_AdrenalThyroidSpleen.T136_b16_Thyroid_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 SL263_b15_RNA_AdrenalThyroidSpleen.T176_b16_Thyroid_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL263_b15_RNA_AdrenalThyroidSpleen.T176_b16_Thyroid_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 SL263_b15_RNA_AdrenalThyroidSpleen.T273_b16_Adr_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL263_b15_RNA_AdrenalThyroidSpleen.T273_b16_Adr_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 SL263_b15_RNA_AdrenalThyroidSpleen.T314_b16_Spleen_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL263_b15_RNA_AdrenalThyroidSpleen.T314_b16_Spleen_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 SL263_b15_RNA_AdrenalThyroidSpleen.T318_b16_Adr_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL263_b15_RNA_AdrenalThyroidSpleen.T318_b16_Adr_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 SL263_b15_RNA_AdrenalThyroidSpleen.T390_b16_Adr_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL263_b15_RNA_AdrenalThyroidSpleen.T390_b16_Adr_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 SL263_b15_RNA_AdrenalThyroidSpleen.T40_b16_Adr_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL263_b15_RNA_AdrenalThyroidSpleen.T40_b16_Adr_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 SL265_b9_RNA_Muscle.T10_b9_Muscle_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-SL265_b9_RNA_Muscle.T10_b9_Muscle_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 SL265_b9_RNA_Muscle.T123_b9_Muscle_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-SL265_b9_RNA_Muscle.T123_b9_Muscle_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 SL265_b9_RNA_Muscle.T161_b9_Muscle_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-SL265_b9_RNA_Muscle.T161_b9_Muscle_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 SL265_b9_RNA_Muscle.T377_b9_Muscle_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-SL265_b9_RNA_Muscle.T377_b9_Muscle_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 SL265_b9_RNA_Muscle.T44_b9_Muscle_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-SL265_b9_RNA_Muscle.T44_b9_Muscle_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 SL265_b9_RNA_Muscle.T61_b9_Muscle_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-SL265_b9_RNA_Muscle.T61_b9_Muscle_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 SL265_b9_RNA_Muscle.T87_b9_Muscle_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-SL265_b9_RNA_Muscle.T87_b9_Muscle_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 SL265_b9_RNA_Muscle.T96_b9_Muscle_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-SL265_b9_RNA_Muscle.T96_b9_Muscle_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 SL254_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/hg38.chrom.sizes sam_reads_genes-SL254_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL255_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/hg38.chrom.sizes sam_reads_genes-SL255_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL256_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/hg38.chrom.sizes sam_reads_genes-SL256_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL257_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/hg38.chrom.sizes sam_reads_genes-SL257_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL258_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/hg38.chrom.sizes sam_reads_genes-SL258_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL259_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/hg38.chrom.sizes sam_reads_genes-SL259_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL260_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/hg38.chrom.sizes sam_reads_genes-SL260_b17_RNA_SpleenThymus.T165_b17_Spleen_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 SL254_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/hg38.chrom.sizes sam_reads_genes-SL254_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL255_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/hg38.chrom.sizes sam_reads_genes-SL255_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL256_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/hg38.chrom.sizes sam_reads_genes-SL256_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL257_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/hg38.chrom.sizes sam_reads_genes-SL257_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL258_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/hg38.chrom.sizes sam_reads_genes-SL258_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL259_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/hg38.chrom.sizes sam_reads_genes-SL259_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL260_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/hg38.chrom.sizes sam_reads_genes-SL260_b17_RNA_SpleenThymus.T233_b17_Thymus_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 SL254_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/hg38.chrom.sizes sam_reads_genes-SL254_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL255_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/hg38.chrom.sizes sam_reads_genes-SL255_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL256_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/hg38.chrom.sizes sam_reads_genes-SL256_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL257_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/hg38.chrom.sizes sam_reads_genes-SL257_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL258_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/hg38.chrom.sizes sam_reads_genes-SL258_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL259_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/hg38.chrom.sizes sam_reads_genes-SL259_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL260_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/hg38.chrom.sizes sam_reads_genes-SL260_b17_RNA_SpleenThymus.T23_b17_Thymus_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 SL254_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/hg38.chrom.sizes sam_reads_genes-SL254_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL255_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/hg38.chrom.sizes sam_reads_genes-SL255_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL256_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/hg38.chrom.sizes sam_reads_genes-SL256_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL257_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/hg38.chrom.sizes sam_reads_genes-SL257_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL258_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/hg38.chrom.sizes sam_reads_genes-SL258_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL259_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/hg38.chrom.sizes sam_reads_genes-SL259_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL260_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/hg38.chrom.sizes sam_reads_genes-SL260_b17_RNA_SpleenThymus.T270_b17_Spleen_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 SL254_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/hg38.chrom.sizes sam_reads_genes-SL254_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL255_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/hg38.chrom.sizes sam_reads_genes-SL255_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL256_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/hg38.chrom.sizes sam_reads_genes-SL256_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL257_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/hg38.chrom.sizes sam_reads_genes-SL257_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL258_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/hg38.chrom.sizes sam_reads_genes-SL258_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL259_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/hg38.chrom.sizes sam_reads_genes-SL259_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL260_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/hg38.chrom.sizes sam_reads_genes-SL260_b17_RNA_SpleenThymus.T314_b17_Spleen_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 SL254_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/hg38.chrom.sizes sam_reads_genes-SL254_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL255_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/hg38.chrom.sizes sam_reads_genes-SL255_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL256_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/hg38.chrom.sizes sam_reads_genes-SL256_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL257_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/hg38.chrom.sizes sam_reads_genes-SL257_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL258_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/hg38.chrom.sizes sam_reads_genes-SL258_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL259_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/hg38.chrom.sizes sam_reads_genes-SL259_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL260_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/hg38.chrom.sizes sam_reads_genes-SL260_b17_RNA_SpleenThymus.T406_b17_Thymus_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 SL254_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/hg38.chrom.sizes sam_reads_genes-SL254_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL255_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/hg38.chrom.sizes sam_reads_genes-SL255_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL256_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/hg38.chrom.sizes sam_reads_genes-SL256_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL257_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/hg38.chrom.sizes sam_reads_genes-SL257_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL258_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/hg38.chrom.sizes sam_reads_genes-SL258_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL259_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/hg38.chrom.sizes sam_reads_genes-SL259_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL260_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/hg38.chrom.sizes sam_reads_genes-SL260_b17_RNA_SpleenThymus.T88_b17_Spleen_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 SL254_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/hg38.chrom.sizes sam_reads_genes-SL254_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL255_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/hg38.chrom.sizes sam_reads_genes-SL255_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL256_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/hg38.chrom.sizes sam_reads_genes-SL256_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL257_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/hg38.chrom.sizes sam_reads_genes-SL257_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL258_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/hg38.chrom.sizes sam_reads_genes-SL258_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL259_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/hg38.chrom.sizes sam_reads_genes-SL259_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL260_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/hg38.chrom.sizes sam_reads_genes-SL260_b17_RNA_SpleenThymus.T90_b17_Thymus_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 SL263_b15_RNA_AdrenalThyroidSpleen.T136_b16_Thyroid_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-SL263_b15_RNA_AdrenalThyroidSpleen.T136_b16_Thyroid_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 SL263_b15_RNA_AdrenalThyroidSpleen.T176_b16_Thyroid_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-SL263_b15_RNA_AdrenalThyroidSpleen.T176_b16_Thyroid_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 SL263_b15_RNA_AdrenalThyroidSpleen.T273_b16_Adr_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-SL263_b15_RNA_AdrenalThyroidSpleen.T273_b16_Adr_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 SL263_b15_RNA_AdrenalThyroidSpleen.T314_b16_Spleen_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-SL263_b15_RNA_AdrenalThyroidSpleen.T314_b16_Spleen_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 SL263_b15_RNA_AdrenalThyroidSpleen.T318_b16_Adr_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-SL263_b15_RNA_AdrenalThyroidSpleen.T318_b16_Adr_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 SL263_b15_RNA_AdrenalThyroidSpleen.T390_b16_Adr_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-SL263_b15_RNA_AdrenalThyroidSpleen.T390_b16_Adr_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 SL263_b15_RNA_AdrenalThyroidSpleen.T40_b16_Adr_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-SL263_b15_RNA_AdrenalThyroidSpleen.T40_b16_Adr_PCW17 -nomulti &