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Old 09-20-2013, 01:31 AM   #1
Location: Sweden

Join Date: Jun 2013
Posts: 51
Exclamation TopHat annotation file issue


I am aligning my RNA-seq data by TopHat and I get an error as following:

[2013-09-20 09:30:16] Creating transcriptome data files..
Error: gtf_to_fasta returned an error.

I have checked the names of gtf and index files are same. Also both files have been downloaded from ensemble (meaning I don't have different format of chromosomes name). When I am using UCSC index and gtf file everything works well. But UCSC doesn't provide genes name but only genes ids. That's why I want to switch to ensembl. I was wondering if you have any idea about this!

Thanks for any help!
rozitaa is offline   Reply With Quote
Old 09-20-2013, 06:25 AM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

If you look in the run log, you'll see the actual command that's executed. Just try executing that yourself to find out what the real error message is. That'll give you a better idea what went wrong.
dpryan is offline   Reply With Quote

annotaion file, tophat

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