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_1_CTCFvalidationRNAseq_170812_S9-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-13004_1_CTCFvalidationRNAseq_170812_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 13004_2_CTCFvalidationRNAseq_170812_S10-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-13004_2_CTCFvalidationRNAseq_170812_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 13006_1_CTCFvalidationRNAseq_170812_S11-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-13006_1_CTCFvalidationRNAseq_170812_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 13006_2_CTCFvalidationRNAseq_170812_S12-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-13006_2_CTCFvalidationRNAseq_170812_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 12040-GH549_1_CTCFvalidationRNAseq_170812_S1-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-12040-GH549_1_CTCFvalidationRNAseq_170812_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 12040-GH549_2_CTCFvalidationRNAseq_170812_S2-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-12040-GH549_2_CTCFvalidationRNAseq_170812_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 12042-GH550_1_CTCFvalidationRNAseq_170812_S3-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-12042-GH550_1_CTCFvalidationRNAseq_170812_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 12042-GH550_2_CTCFvalidationRNAseq_170812_S4-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-12042-GH550_2_CTCFvalidationRNAseq_170812_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 14376-GH551_1_CTCFvalidationRNAseq_170812_S5-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-14376-GH551_1_CTCFvalidationRNAseq_170812_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 14376-GH551_2_CTCFvalidationRNAseq_170812_S6-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-14376-GH551_2_CTCFvalidationRNAseq_170812_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 14377-GH552_1_CTCFvalidationRNAseq_170812_S7-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-14377-GH552_1_CTCFvalidationRNAseq_170812_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 14377-GH552_2_CTCFvalidationRNAseq_170812_S8-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-14377-GH552_2_CTCFvalidationRNAseq_170812_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_1_CTCFvalidationRNAseq_170812_S13-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-N4293_1_CTCFvalidationRNAseq_170812_S13 -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_2_CTCFvalidationRNAseq_170812_S14-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-N4293_2_CTCFvalidationRNAseq_170812_S14 -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 N4871_1_CTCFvalidationRNAseq_170812_S15-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-N4871_1_CTCFvalidationRNAseq_170812_S15 -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 N4871_2_CTCFvalidationRNAseq_170812_S16-2x50mers-STAR2.5.3a-GENCODEV19/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-N4871_2_CTCFvalidationRNAseq_170812_S16 -nomulti &