Question: Where can I download homo sapiens gene locations file including ensembl gene id, chr, start and end?
0
gravatar for Huichen03
5 months ago by
Huichen0310
Huichen0310 wrote:

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 • 307 views
ADD COMMENTlink modified 5 months ago by JJ350 • written 5 months ago by Huichen0310
1
gravatar for Emily_Ensembl
5 months ago by
Emily_Ensembl16k
EMBL-EBI
Emily_Ensembl16k wrote:

GTF or GFF?

ADD COMMENTlink written 5 months ago by Emily_Ensembl16k

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 REPLYlink written 5 months ago by dariober9.5k

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

ADD REPLYlink written 5 months ago by genomax57k

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 REPLYlink written 5 months ago by dariober9.5k

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 REPLYlink written 5 months ago by Mike Smith870

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

ADD REPLYlink written 5 months ago by genomax57k
0
gravatar for genomax
5 months ago by
genomax57k
United States
genomax57k wrote:

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

ADD COMMENTlink modified 5 months ago • written 5 months ago by genomax57k
0
gravatar for JJ
5 months ago by
JJ350
JJ350 wrote:

Gencode gtf or gff files

ADD COMMENTlink written 5 months ago by JJ350
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