python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py Decaurelia.mito/Decaurelia.mito.60aa-ORF.renamed.min100aa.noORF-no-hit.bed 0 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 Paramecium_decaurelia-223-GSF1240-DE1_S2-2x80-TopHat-2.0.8-minIntron10-genome+mito/accepted_hits.mito.60aa-ORF.renamed.min100aa.noORF-no-hit.RPKM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py Dodecaurelia.mito/Dodecaurelia.mito.60aa-ORF.renamed.min100aa.noORF-no-hit.bed 0 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 Paramecium_dodecaurelia-274-GSF1240-DO1_S1-2x80-TopHat-2.0.8-minIntron10-genome+mito/accepted_hits.mito.60aa-ORF.renamed.min100aa.noORF-no-hit.RPKM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py Jenningsi.mito/Jenningsi.mito.60aa-ORF.renamed.min100aa.noORF-no-hit.bed 0 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 Paramecium_jenningsi-M-GSF1240-J1_S6-2x80-TopHat-2.0.8-minIntron10-genome+mito/accepted_hits.mito.60aa-ORF.renamed.min100aa.noORF-no-hit.RPKM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py Novaurelia.mito/Novaurelia.mito.60aa-ORF.renamed.min100aa.noORF-no-hit.bed 0 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 Paramecium_novaurelia-TE-GSF1240-N1_S5-2x80-TopHat-2.0.8-minIntron10-genome+mito/accepted_hits.mito.60aa-ORF.renamed.min100aa.noORF-no-hit.RPKM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py Quadecaurelia.mito/Quadecaurelia.mito.60aa-ORF.renamed.min100aa.noORF-no-hit.bed 0 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 Paramecium_quadecaurelia-N1A-GSF1240-DE1_S2-2x80-TopHat-2.0.8-minIntron10-genome+mito/accepted_hits.mito.60aa-ORF.renamed.min100aa.noORF-no-hit.RPKM