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Resource For Gff-Files?

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.

rna gtf gff
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updated by Ian Ian • written by Student • Student

2 answers

ensembl.org - ensembl human gtf

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written by Caddymob Caddymob

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

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written by Caddymob Caddymob

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

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written by Student • Student

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

I hope it helps!

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written by Ian Ian

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

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written by brentp brentp

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.

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written by Malachi Griffith Malachi Griffith

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