python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.gtf ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes  sam_reads_in_genes-ME49.Bz.A-SRX9295974 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.gtf ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes  sam_reads_in_genes-ME49.Bz.B-SRX9295975 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.gtf ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes  sam_reads_in_genes-ME49.Tz.A-SRX9295976 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.gtf ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes  sam_reads_in_genes-ME49.Tz.B-SRX9295977 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.gtf RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes  sam_reads_in_genes-RH.Tz.A-SRX9295978 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.gtf RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes  sam_reads_in_genes-RH.Tz.B-SRX9295979 -nomulti