[BioC] Quick question about Chromosome names using Tophat2 and Cufflinks w/Ensembl NCBIM37

[James W. MacDonald]

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/Ensembl/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/Annotation/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!
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099