Resource For Gff-Files?
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12.9 years ago
Student ▴ 90

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 • 4.5k views
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12.9 years ago
Caddymob ★ 1.0k

ensembl.org - ensembl human gtf

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

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

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12.9 years ago
Ian 6.1k

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

I hope it helps!

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

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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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