Question: Where can I download homo sapiens gene locations file including ensembl gene id, chr, start and end?
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gravatar for xiaohuichen03
28 days ago by
xiaohuichen030 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 • 153 views
ADD COMMENTlink modified 27 days ago by JJ300 • written 28 days ago by xiaohuichen030
1
gravatar for Emily_Ensembl
27 days ago by
Emily_Ensembl14k
EMBL-EBI
Emily_Ensembl14k wrote:

GTF or GFF?

ADD COMMENTlink written 27 days ago by Emily_Ensembl14k

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 27 days ago by dariober9.1k

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 27 days ago by genomax47k

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 27 days ago by dariober9.1k

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 27 days ago by Mike Smith640

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

ADD REPLYlink written 27 days ago by genomax47k
0
gravatar for genomax
28 days ago by
genomax47k
United States
genomax47k wrote:

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

ADD COMMENTlink modified 28 days ago • written 28 days ago by genomax47k
0
gravatar for JJ
27 days ago by
JJ300
JJ300 wrote:

Gencode gtf or gff files

ADD COMMENTlink written 27 days ago by JJ300
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