python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Amphibians/xenTro10/2022-11-17-refSeq.gtf Adult-female-WTSSseq-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Amphibians/xenTro10/xenTro10.chrom.sizes  sam_reads_in_genes-Adult-female-WTSSseq-pooled -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Amphibians/xenTro10/2022-11-17-refSeq.gtf Adult-femalepool-CAGEseq-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Amphibians/xenTro10/xenTro10.chrom.sizes  sam_reads_in_genes-Adult-femalepool-CAGEseq -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Amphibians/xenTro10/2022-11-17-refSeq.gtf Adult-male-WTSSseq-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Amphibians/xenTro10/xenTro10.chrom.sizes  sam_reads_in_genes-Adult-male-WTSSseq-pooled -nomulti