python /home/users/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Paramecium_decaurelia-223/pdecaurelia_223_annotation_v1.0.gtf Paramecium_decaurelia-223-GSF1240-DE1_S2-2x80-TopHat-2.0.8-minIntron10-genome+mito/accepted_hits.bam /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Paramecium_decaurelia-223/pdecaurelia_mac_223_v1.0+chrM.chrom.sizes sam_reads_genes-Paramecium_decaurelia-223-GSF1240-DE1_S2 -nomulti
python /home/users/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Paramecium_dodecaurelia-274/pdodecaurelia_274_annotation_v1.0.gtf Paramecium_dodecaurelia-274-GSF1240-DO1_S1-2x80-TopHat-2.0.8-minIntron10-genome+mito/accepted_hits.bam /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Paramecium_dodecaurelia-274/pdodecaurelia_mac_274_v1.0+chrM.chrom.sizes sam_reads_genes-Paramecium_dodecaurelia-274-GSF1240-DO1_S1 -nomulti
python /home/users/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Paramecium_jenningsi-M/pjenningsi_M_annotation_v1.0.gtf Paramecium_jenningsi-M-GSF1240-J1_S6-2x80-TopHat-2.0.8-minIntron10-genome+mito/accepted_hits.bam /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Paramecium_jenningsi-M/pjenningsi_mac_M_v1.0+chrM.chrom.sizes sam_reads_genes-Paramecium_jenningsi-M-GSF1240-J1_S6 -nomulti
python /home/users/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Paramecium_novaurelia-TE/pnovaurelia_TE_annotation_v1.0.gtf Paramecium_novaurelia-TE-GSF1240-N1_S5-2x80-TopHat-2.0.8-minIntron10-genome+mito/accepted_hits.bam /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Paramecium_novaurelia-TE/pnovaurelia_mac_TE_v1.0+chrM.chrom.sizes sam_reads_genes-Paramecium_novaurelia-TE-GSF1240-N1_S5 -nomulti
python /home/users/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Paramecium_quadecaurelia-N1A/pquadecaurelia_NiA_annotation_v1.0.gtf Paramecium_quadecaurelia-N1A-GSF1240-DE1_S2-2x80-TopHat-2.0.8-minIntron10-genome+mito/accepted_hits.bam /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Paramecium_quadecaurelia-N1A/pquadecaurelia_mac_NiA_v1.0+chrM.chrom.sizes sam_reads_genes-Paramecium_quadecaurelia-N1A-GSF1240-DE1_S2 -nomulti