python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a-aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-13004-rep1-S1 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 13004-rep2-S2-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a-aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-13004-rep2-S2 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 13006-rep1-S3-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a-aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-13006-rep1-S3 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 13006-rep2-S4-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a-aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-13006-rep2-S4 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 13189-rep1-JT_CTCFvalidationRNAseq_170303_S9-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a-aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-13189-rep1-JT_CTCFvalidationRNAseq_170303_S9 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 13189-rep2-JT_CTCFvalidationRNAseq_170303_S10-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a-aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-13189-rep2-JT_CTCFvalidationRNAseq_170303_S10 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 13190-rep1-JT_CTCFvalidationRNAseq_170303_S11-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a-aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-13190-rep1-JT_CTCFvalidationRNAseq_170303_S11 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 13190-rep2-JT_CTCFvalidationRNAseq_170303_S12-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a-aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-13190-rep2-JT_CTCFvalidationRNAseq_170303_S12 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 15171-rep1-JT_CTCFvalidationRNAseq_170303_S5-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a-aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-15171-rep1-JT_CTCFvalidationRNAseq_170303_S5 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 15171-rep2-JT_CTCFvalidationRNAseq_170303_S6-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a-aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-15171-rep2-JT_CTCFvalidationRNAseq_170303_S6 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 15173-rep1-JT_CTCFvalidationRNAseq_170303_S7-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a-aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-15173-rep1-JT_CTCFvalidationRNAseq_170303_S7 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 15173-rep2-JT_CTCFvalidationRNAseq_170303_S8-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a-aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-15173-rep2-JT_CTCFvalidationRNAseq_170303_S8 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf N4293-rep1-JT_CTCFvalidationRNAseq_170303_S1-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a-aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-N4293-rep1-JT_CTCFvalidationRNAseq_170303_S1 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf N4293-rep1-S5-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a-aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-N4293-rep1-S5 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf N4293-rep2-JT_CTCFvalidationRNAseq_170303_S2-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a-aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-N4293-rep2-JT_CTCFvalidationRNAseq_170303_S2 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf N4293-rep2-S6-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a-aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-N4293-rep2-S6 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf N4371-rep1-JT_CTCFvalidationRNAseq_170303_S3-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a-aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-N4371-rep1-JT_CTCFvalidationRNAseq_170303_S3 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf N4371-rep1-S7-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a-aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-N4371-rep1-S7 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf N4371-rep2-JT_CTCFvalidationRNAseq_170303_S4-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a-aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-N4371-rep2-JT_CTCFvalidationRNAseq_170303_S4 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf N4371-rep2-S8-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a-aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-N4371-rep2-S8 -nomulti &