Question: How to get gene annotation for a list of genes
0
gravatar for wstla27
14 months ago by
wstla2710
wstla2710 wrote:

I have a list of genes with their ensembl ids. I want to get their positions on chromosomes or functional annotations, so that I can use bedtools to align them with some bam files and get their gene expressions (counts). Is there anyway that I can do this in bulk instead of one by one?

(I looked at SnpEff but I don’t think that’s what I want. )

Many thanks!

gene • 361 views
ADD COMMENTlink written 14 months ago by wstla2710
3
gravatar for RamRS
14 months ago by
RamRS30k
Baylor College of Medicine, Houston, TX
RamRS30k wrote:

I'm assuming these are human genes.

You can use various R packages to get these data dimensions - org.Hs.eg.db, biomaRt, TxDb (I think), etc. search for "get sequence from gene symbol" (say) to get a more concrete lead on the package to try.

ADD COMMENTlink written 14 months ago by RamRS30k

Tried biomaRT, worked perfectly! Thanks a lot!

ADD REPLYlink written 14 months ago by wstla2710

Glad it helped. If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they all work.

Upvote|Bookmark|Accept

ADD REPLYlink written 14 months ago by RamRS30k
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