/oak/stanford/groups/akundaje/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 8 --GTF Decaurelia.mito/Decaurelia.mito.60aa-ORF.renamed.min100aa.noORF-no-hit.gtf --output-dir Paramecium_decaurelia-223-GSF1240-DE1_S2-2x80-TopHat-2.0.8-minIntron10-genome+mito/Cufflinks-2.0.2-mito.60aa-ORF.renamed.min100aa.noORF-no-hit Paramecium_decaurelia-223-GSF1240-DE1_S2-2x80-TopHat-2.0.8-minIntron10-genome+mito/accepted_hits.bam
/oak/stanford/groups/akundaje/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 8 --GTF Dodecaurelia.mito/Dodecaurelia.mito.60aa-ORF.renamed.min100aa.noORF-no-hit.gtf --output-dir Paramecium_dodecaurelia-274-GSF1240-DO1_S1-2x80-TopHat-2.0.8-minIntron10-genome+mito/Cufflinks-2.0.2-mito.60aa-ORF.renamed.min100aa.noORF-no-hit Paramecium_dodecaurelia-274-GSF1240-DO1_S1-2x80-TopHat-2.0.8-minIntron10-genome+mito/accepted_hits.bam
/oak/stanford/groups/akundaje/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 8 --GTF Jenningsi.mito/Jenningsi.mito.60aa-ORF.renamed.min100aa.noORF-no-hit.gtf --output-dir Paramecium_jenningsi-M-GSF1240-J1_S6-2x80-TopHat-2.0.8-minIntron10-genome+mito/Cufflinks-2.0.2-mito.60aa-ORF.renamed.min100aa.noORF-no-hit Paramecium_jenningsi-M-GSF1240-J1_S6-2x80-TopHat-2.0.8-minIntron10-genome+mito/accepted_hits.bam
/oak/stanford/groups/akundaje/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 8 --GTF Novaurelia.mito/Novaurelia.mito.60aa-ORF.renamed.min100aa.noORF-no-hit.gtf --output-dir Paramecium_novaurelia-TE-GSF1240-N1_S5-2x80-TopHat-2.0.8-minIntron10-genome+mito/Cufflinks-2.0.2-mito.60aa-ORF.renamed.min100aa.noORF-no-hit Paramecium_novaurelia-TE-GSF1240-N1_S5-2x80-TopHat-2.0.8-minIntron10-genome+mito/accepted_hits.bam
/oak/stanford/groups/akundaje/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 8 --GTF Quadecaurelia.mito/Quadecaurelia.mito.60aa-ORF.renamed.min100aa.noORF-no-hit.gtf --output-dir Paramecium_quadecaurelia-N1A-GSF1240-DE1_S2-2x80-TopHat-2.0.8-minIntron10-genome+mito/Cufflinks-2.0.2-mito.60aa-ORF.renamed.min100aa.noORF-no-hit Paramecium_quadecaurelia-N1A-GSF1240-DE1_S2-2x80-TopHat-2.0.8-minIntron10-genome+mito/accepted_hits.bam