Where can I download homo sapiens gene locations file including ensembl gene id, chr, start and end?
3
0
Entering edit mode
6.0 years ago
Huichen03 ▴ 20

I am trying to use GRange for mapping snps to gene around 100kb. But I do not know how to download homo sapiens gene locations file including ensembl gene id, chr, start and end?

Thank you in advance!

SNP biomart gene • 2.2k views
ADD COMMENT
1
Entering edit mode
6.0 years ago
Emily 23k

GTF or GFF?

ADD COMMENT
0
Entering edit mode

Maybe it's worth pointing out that GTF is identical to GFF2 and GFF2 is deprecated. So, other things being equal, go for GFF3, often referred to as just GFF. Did I get it right?

ADD REPLY
0
Entering edit mode

Using BioMart is still the easy way since there would be further manipulations needed to get the information OP wants from these files.

ADD REPLY
0
Entering edit mode

Hi genomax- I agree. However, I think the advantage of going for a direct link is that you can stick in your documentation or script something like wget ftp://ftp.ensembl.org/pub/release-92/gff3/homo_sapiens/Homo_sapiens.GRCh38.92.chr.gff3.gz and that makes self-explanatory what data you are referring to. In my experience (maybe it's just me of course...!) with layers like BioMart either you have to be quite diligent in documenting what you have done or you end up with data that you can be sure how you got.

ADD REPLY
0
Entering edit mode

You can use a programmatic interface to BioMart like biomaRt and then your script records the steps you took to get the data out.

ADD REPLY
0
Entering edit mode

dariober : Agreed. Depending on how savvy OP is they can choose an appropriate method to follow.

ADD REPLY
0
Entering edit mode
6.0 years ago
GenoMax 141k

Using BioMart at Ensembl. Here is a link for a BioMart video tutorial.

ADD COMMENT
0
Entering edit mode
6.0 years ago
JJ ▴ 670

Gencode gtf or gff files

ADD COMMENT

Login before adding your answer.

Traffic: 1330 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6