Difficulty in getting GTF file from iGenomes

Question

[nazaninhoseinkhan]

Dear all,

I need to use GTF annotation file for my RNASeq project. I downloaded GTF for human from ensembl, but it did not work well when I used it in Cufflinks. In fact all FPKMs were recorded as zero.

Some one advised me to use gtf annotation from iGenomes.

Unfortunately I faced with difficulty in downloading it from iGenomes.

Can anyone tell me what should I do?

can I download this file from any other sources? or can anyone send it to me?

I appreciate any help in advance Nazanin

[WouterDeCoster]

What goes wrong when trying to download?

[nazaninhoseinkhan]

Thanks for your response. I could get it from Galaxy.

Answer 1

[Devon Ryan]

The ones available from iGenome are just slightly modified version of what you get from Ensembl or UCSC. Most likely you aligned against a genome from UCSC, where the chromosome names differ from those used by Ensembl (e.g., "chr1" rather than "1"). Check that to see if it's happening.

[nazaninhoseinkhan]

Thanks. my problem was solved