Converting chromosome names in gtf file

[cnyh]

The TopHat manual tells me that "the values in the first column of the provided GTF/GFF file [...] must match the name of the reference sequence in the Bowtie index you are using with TopHat."

I checked my Homo_sapiens.GRCh37.70.gtf file, and found that the first column contained names like "HG104_HG975_PATCH". The command "bowtie2-inspect --names hg19" in the folder containing the Bowtie2 indexes showed me names like "chr1" etc.

My question is: how do I get this changed? Do I need to look for another Ensembl gtf file?

[aggp11]

Hi,

Could you paste the first 5-10 lines of your GTF file here?