python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py BL198_SHAREseq_A549_p53_RNA_1_3.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-BL198_SHAREseq_A549_p53_RNA_1_3 -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 BL199_SHAREseq_A549_p53_RNA_1_4.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-BL199_SHAREseq_A549_p53_RNA_1_4 -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 BL200_SHAREseq_A549_p53_RNA_2_1.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-BL200_SHAREseq_A549_p53_RNA_2_1 -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 BL201_SHAREseq_A549_p53_RNA_2_2.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-BL201_SHAREseq_A549_p53_RNA_2_2 -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 BL198_SHAREseq_A549_p53_RNA_1_3.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-BL198_SHAREseq_A549_p53_RNA_1_3 -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 BL199_SHAREseq_A549_p53_RNA_1_4.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-BL199_SHAREseq_A549_p53_RNA_1_4 -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 BL200_SHAREseq_A549_p53_RNA_2_1.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-BL200_SHAREseq_A549_p53_RNA_2_1 -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 BL201_SHAREseq_A549_p53_RNA_2_2.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-BL201_SHAREseq_A549_p53_RNA_2_2 -nomulti &