TopHat annotation file issue

[rozitaa]

Hi,

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..
[FAILED]
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!

[dpryan]

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.