Tophat2 cmd: tophat2 -o path/to --transcriptome-index=/Mus_musculus_Ensembl_NCBIM37/Mus_musculus/Ensem bl/NCBIM37/Annotation/Genes/genes /Mus_musculus_Ensembl_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Sequence/Bo wtie2Index/genome 001.fastq.gz Cufflinks cmd: cufflinks --output-dir path/to --GTF-guide /Mus_musculus_Ensembl_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Annotation/ Archives/archive-2013-03-06-18-55-12/Genes/genes.gtf --frag-bias-correct /Mus_musculus_Ensembl_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Sequence/Bo wtie2Index/genome.fa --multi-read-correct --upper-quartile-norm --verbose accepted_hits.bam Cufflinks then names the chromosomes like this, is that correct? How can I control this or alter it? 20: MT 10: 18 11: 19 4: 12 5: 13 2: 10 3: 11 8: 16 9: 17 6: 14 7: 15 22: Y 21: X 19: 9 18: 8 17: 7 16: 6 15: 5 14: 4 13: 3 12: 2 1: 1 Thank you!

Hi Sindre, Why are you asking about tophat and cufflinks on a BioC listserv? These are not part of BioC, nor are they even R packages. In addition, they have their own list where you can ask questions. Best, Jim On 3/10/2014 3:36 AM, Sindre Lee wrote: > Tophat2 cmd: > > tophat2 -o path/to > --transcriptome-index=/Mus_musculus_Ensembl_NCBIM37/Mus_musculus/Ens embl/NCBIM37/Annotation/Genes/genes > /Mus_musculus_Ensembl_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Sequence/ Bowtie2Index/genome > 001.fastq.gz > > Cufflinks cmd: > > cufflinks --output-dir path/to --GTF-guide > /Mus_musculus_Ensembl_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Annotatio n/Archives/archive-2013-03-06-18-55-12/Genes/genes.gtf > --frag-bias-correct > /Mus_musculus_Ensembl_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Sequence/ Bowtie2Index/genome.fa > --multi-read-correct --upper-quartile-norm --verbose accepted_hits.bam > > Cufflinks then names the chromosomes like this, is that correct? How > can I control this or alter it? > > 20: MT > 10: 18 > 11: 19 > 4: 12 > 5: 13 > 2: 10 > 3: 11 > 8: 16 > 9: 17 > 6: 14 > 7: 15 > 22: Y > 21: X > 19: 9 > 18: 8 > 17: 7 > 16: 6 > 15: 5 > 14: 4 > 13: 3 > 12: 2 > 1: 1 > > Thank you! > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099