python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf CA1_10F-CAGE-GSM2323923-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-CA1_10F-CAGE-GSM2323923 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf CA1_10M-CAGE-GSM2323924-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-CA1_10M-CAGE-GSM2323924 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf CA1_1F-CAGE-GSM2323919-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-CA1_1F-CAGE-GSM2323919 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf CA1_1M-CAGE-GSM2323920-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-CA1_1M-CAGE-GSM2323920 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf CA1_20F-CAGE-GSM2323925-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-CA1_20F-CAGE-GSM2323925 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf CA1_20M-CAGE-GSM2323926-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-CA1_20M-CAGE-GSM2323926 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf CA1_4F-CAGE-GSM2323921-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-CA1_4F-CAGE-GSM2323921 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf CA1_4M-CAGE-GSM2323922-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-CA1_4M-CAGE-GSM2323922 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf CB_10F-CAGE-GSM2323939-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-CB_10F-CAGE-GSM2323939 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf CB_10M-CAGE-GSM2323940-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-CB_10M-CAGE-GSM2323940 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf CB_1F-CAGE-GSM2323935-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-CB_1F-CAGE-GSM2323935 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf CB_1M-CAGE-GSM2323936-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-CB_1M-CAGE-GSM2323936 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf CB_20F-CAGE-GSM2323941-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-CB_20F-CAGE-GSM2323941 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf CB_20M-CAGE-GSM2323942-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-CB_20M-CAGE-GSM2323942 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf CB_4F-CAGE-GSM2323937-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-CB_4F-CAGE-GSM2323937 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf CB_4M-CAGE-GSM2323938-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-CB_4M-CAGE-GSM2323938 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf DG_10F-CAGE-GSM2323931-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-DG_10F-CAGE-GSM2323931 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf DG_10M-CAGE-GSM2323932-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-DG_10M-CAGE-GSM2323932 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf DG_1F-CAGE-GSM2323927-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-DG_1F-CAGE-GSM2323927 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf DG_1M-CAGE-GSM2323928-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-DG_1M-CAGE-GSM2323928 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf DG_20F-CAGE-GSM2323933-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-DG_20F-CAGE-GSM2323933 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf DG_20M-CAGE-GSM2323934-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-DG_20M-CAGE-GSM2323934 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf DG_4F-CAGE-GSM2323929-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-DG_4F-CAGE-GSM2323929 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf DG_4M-CAGE-GSM2323930-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-DG_4M-CAGE-GSM2323930 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf OC_10F-CAGE-GSM2323947-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-OC_10F-CAGE-GSM2323947 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf OC_10M-CAGE-GSM2323948-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-OC_10M-CAGE-GSM2323948 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf OC_1F-CAGE-GSM2323943-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-OC_1F-CAGE-GSM2323943 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf OC_1M-CAGE-GSM2323944-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-OC_1M-CAGE-GSM2323944 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf OC_20F-CAGE-GSM2323949-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-OC_20F-CAGE-GSM2323949 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf OC_20M-CAGE-GSM2323950-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-OC_20M-CAGE-GSM2323950 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf OC_4F-CAGE-GSM2323945-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-OC_4F-CAGE-GSM2323945 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf OC_4M-CAGE-GSM2323946-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-OC_4M-CAGE-GSM2323946 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf PCC_10F-CAGE-GSM2323899-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-PCC_10F-CAGE-GSM2323899 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf PCC_10M-CAGE-GSM2323900-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-PCC_10M-CAGE-GSM2323900 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf PCC_1F-CAGE-GSM2323895-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-PCC_1F-CAGE-GSM2323895 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf PCC_1M-CAGE-GSM2323896-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-PCC_1M-CAGE-GSM2323896 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf PCC_20F-CAGE-GSM2323901-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-PCC_20F-CAGE-GSM2323901 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf PCC_20M-CAGE-GSM2323902-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-PCC_20M-CAGE-GSM2323902 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf PCC_4F-CAGE-GSM2323897-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-PCC_4F-CAGE-GSM2323897 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf PCC_4M-CAGE-GSM2323898-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-PCC_4M-CAGE-GSM2323898 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf PC_10F-CAGE-GSM2323915-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-PC_10F-CAGE-GSM2323915 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf PC_10M-CAGE-GSM2323916-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-PC_10M-CAGE-GSM2323916 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf PC_1F-CAGE-GSM2323911-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-PC_1F-CAGE-GSM2323911 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf PC_1M-CAGE-GSM2323912-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-PC_1M-CAGE-GSM2323912 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf PC_20F-CAGE-GSM2323917-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-PC_20F-CAGE-GSM2323917 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf PC_20M-CAGE-GSM2323918-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-PC_20M-CAGE-GSM2323918 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf PC_4F-CAGE-GSM2323913-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-PC_4F-CAGE-GSM2323913 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf PC_4M-CAGE-GSM2323914-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-PC_4M-CAGE-GSM2323914 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf PFC_10F-CAGE-GSM2323891-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-PFC_10F-CAGE-GSM2323891 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf PFC_10M-CAGE-GSM2323892-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-PFC_10M-CAGE-GSM2323892 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf PFC_1F-CAGE-GSM2323887-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-PFC_1F-CAGE-GSM2323887 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf PFC_1M-CAGE-GSM2323888-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-PFC_1M-CAGE-GSM2323888 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf PFC_20F-CAGE-GSM2323893-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-PFC_20F-CAGE-GSM2323893 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf PFC_20M-CAGE-GSM2323894-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-PFC_20M-CAGE-GSM2323894 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf PFC_4F-CAGE-GSM2323889-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-PFC_4F-CAGE-GSM2323889 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf PFC_4M-CAGE-GSM2323890-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-PFC_4M-CAGE-GSM2323890 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf TC_10F-CAGE-GSM2323907-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-TC_10F-CAGE-GSM2323907 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf TC_10M-CAGE-GSM2323908-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-TC_10M-CAGE-GSM2323908 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf TC_1F-CAGE-GSM2323903-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-TC_1F-CAGE-GSM2323903 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf TC_1M-CAGE-GSM2323904-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-TC_1M-CAGE-GSM2323904 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf TC_20F-CAGE-GSM2323909-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-TC_20F-CAGE-GSM2323909 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf TC_20M-CAGE-GSM2323910-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-TC_20M-CAGE-GSM2323910 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf TC_4F-CAGE-GSM2323905-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-TC_4F-CAGE-GSM2323905 -nomulti python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.gtf TC_4M-CAGE-GSM2323906-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Macaca_mulatta-Mmul_10/GCF_003339765.1_Mmul_10_genomic.chrom.sizes sam_reads_in_genes-TC_4M-CAGE-GSM2323906 -nomulti