python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Cryptococcus_neoformans/Cryptococcus_neoformans.GCA_000091045.1.20.fixed.gtf TSS_tur1delta_30E_merged-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Cryptococcus_neoformans/Cryptococcus_neoformans.GCA_000091045.1.20.chrom.sizes  sam_reads_in_genes-TSS_tur1delta_30E_merged -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Cryptococcus_neoformans/Cryptococcus_neoformans.GCA_000091045.1.20.fixed.gtf TSS_tur1delta_30E_rep_1-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Cryptococcus_neoformans/Cryptococcus_neoformans.GCA_000091045.1.20.chrom.sizes  sam_reads_in_genes-TSS_tur1delta_30E_rep_1 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Cryptococcus_neoformans/Cryptococcus_neoformans.GCA_000091045.1.20.fixed.gtf TSS_tur1delta_30E_rep_2-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Cryptococcus_neoformans/Cryptococcus_neoformans.GCA_000091045.1.20.chrom.sizes  sam_reads_in_genes-TSS_tur1delta_30E_rep_2 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Cryptococcus_neoformans/Cryptococcus_neoformans.GCA_000091045.1.20.fixed.gtf TSS_tur1delta_30E_rep_3-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Cryptococcus_neoformans/Cryptococcus_neoformans.GCA_000091045.1.20.chrom.sizes  sam_reads_in_genes-TSS_tur1delta_30E_rep_3 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Cryptococcus_neoformans/Cryptococcus_neoformans.GCA_000091045.1.20.fixed.gtf TSS_tur1delta_30S_merged-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Cryptococcus_neoformans/Cryptococcus_neoformans.GCA_000091045.1.20.chrom.sizes  sam_reads_in_genes-TSS_tur1delta_30S_merged -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Cryptococcus_neoformans/Cryptococcus_neoformans.GCA_000091045.1.20.fixed.gtf TSS_tur1delta_30S_rep_1-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Cryptococcus_neoformans/Cryptococcus_neoformans.GCA_000091045.1.20.chrom.sizes  sam_reads_in_genes-TSS_tur1delta_30S_rep_1 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Cryptococcus_neoformans/Cryptococcus_neoformans.GCA_000091045.1.20.fixed.gtf TSS_tur1delta_30S_rep_2-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Cryptococcus_neoformans/Cryptococcus_neoformans.GCA_000091045.1.20.chrom.sizes  sam_reads_in_genes-TSS_tur1delta_30S_rep_2 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Cryptococcus_neoformans/Cryptococcus_neoformans.GCA_000091045.1.20.fixed.gtf TSS_tur1delta_30S_rep_3-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Cryptococcus_neoformans/Cryptococcus_neoformans.GCA_000091045.1.20.chrom.sizes  sam_reads_in_genes-TSS_tur1delta_30S_rep_3 -nomulti