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!
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!
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