GTF annotation file for Human

Question

[M K]

I want to run Tophat and I need to use the -G option to provide the Human annotation file .GTF file in my command. I looked at the ensembl website http://uswest.ensembl.org/info/data/ftp/index.html

but I don't know which one is the annotation file. Also Is there any other place to get the human annotation file

Answer 1

[Ashutosh Pandey]

Go to http://www.ensembl.org/info/data/ftp/index.html

Go to GTF folder for human and download

ftp://ftp.ensembl.org/pub/release-75/gtf/homo_sapiens/Homo_sapiens.GRCh37.75.gtf.gz

[Dan D]

You pasted the same link he did.

[Ashutosh Pandey]

Yup I didn't realize that. I have corrected it now.

[M K]

Do you mean the one under Gene sets tab which is 37..5 MB

Answer 2

[Dan D]

You must have glanced right over it. It's on the table in the link you provided under the "Gene Sets" Column in the middle. Here's a direct link to the folder:

ftp://ftp.ensembl.org/pub/release-75/gtf/homo_sapiens

[Bioinformatist Newbie]

Hi Dan, Can you please guide me where I can find gtf file for hg19. I have tried GRCh37.82 and GRCh38.84 but I don't get any features in my raw count file. I am using Encode RNA-seq data (alignment.bam file) and htseq-count for getting the raw counts. Thanks

[miniyad8100]

how did you get GTF file for hg19 ? please let me know. or someone else could help.

[M K]

Thanks Deedee, I got it but is there any difference between GRCh37.0 and GRCh37.75 because I am looking for GRCh37.0 to complete my friend previous work (he used GRCh37.0). so if there is a difference when can I find this old version of the annotation.

[Dan D]

The number after the last dot is the release number. There's no release 0. Are you thinking of the release 55 version (the first "GRCh37", which officially has no suffix), which was succeeded by GRCh37.p3 in June of 2011?

[M K]

Yes that is I need

[M K]

I visited the this link but how can I download this one.

[Dan D]

What's "this one"? GRCh37 from July 2009? N/m, safe to assume it's the original GRCh37.

[Dan D]

Here is the link to the GRCh37 GTF file:

ftp://ftp.ensembl.org/pub/release-55/gtf/homo_sapiens/