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 BMMC_single_donor_RNA.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-BMMC_single_donor_RNA -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py BMMC_single_donor_RNA.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-BMMC_single_donor_RNA -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools