Resource For Gff-Files?

Question

[Student]

Dear Community,

I need .GFF files for HTSeq (htseq-count). What is the easiest option to get a gff file for human? Is there any download available?

Thank you very much.

Answer 1

[Caddymob]

ensembl.org - ensembl human gtf

[Caddymob]

You can also use the table browser in UCSC if you like

[Student]

Oh, it is the same as GTF? Thanks. Why do the files downloaded from UCSC and Ensembl look quite different?

Answer 2

[Ian]

Illumina iGenomes has lots of GTF files (linked from Cufflinks).

I hope it helps!

[brentp]

I didn't know about "iGenomes". thanks.

[Malachi Griffith]

Note that these "annotation files are augmented with the tss_id and p_id GTF attributes that Cufflinks needs to perform differential splicing, CDS output, and promoter user analysis."

For that reason, this may be a better source than Ensembl.