How to get gene annotation for a list of genes

Question

[wstla27]

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!

Answer 1

[Ram]

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.

[wstla27]

Tried biomaRT, worked perfectly! Thanks a lot!

[Ram]

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.