How to get gene annotation for a list of genes

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

• 1,714 views • link

written 7.1 years ago by wstla27 •

1 answer

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.

• 0 views • link

written 7.1 years ago by Ram

Tried biomaRT, worked perfectly! Thanks a lot!

• 0 views • link

written 7.0 years ago by wstla27 •

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

• 0 views • link

written 7.0 years ago by Ram

More posts like this

Integration of RNA seq data aligned to different reference genome versions
written 3.4 years ago by susibing •

Hi all, I would like to integrate a bulk RNA seq and an scRNA seq dataset. The data was already provided as count matrices, but …
Output gene symbol instead of ENST ID in Kallisto
written 4.1 years ago by smurph50 •

My goal is to get a counts matrix with gene symbols from bulk RNA seq data using Kallisto. I ran kallisto and got an abundance.tsv …
InterPro Names from ID (Blast2Go)
written 6.3 years ago by brittanymlebert •

Hello, I ran functional annotations on a genome using InterProScan through Blast2Go. However, the output only shows the InterPro IDs instead of the actual names …
How to get certain gene expressions from bam files
written 7.1 years ago by wstla27 •

I have a list of target genes (with their ensembl ids) and a bunch of .bam files from 1000 genome (https://www.ebi.ac.uk/arrayexpress/files/E-GEUV-1/processed/). Is it possible to …
Different Ensembl Ids point to the same gene symbol.
written 7.1 years ago by elefth.pavlos •

Hi all, I have a matrix with RNA-seq counts of reads. Ensemble gene IDs in rows, samples in columns. I want to check for differential …
R package to annotate and explore effect of biases in RNA Seq
written 8.0 years ago by User 7754

I was wondering if anybody knows about an R package to do usual annotations of regions (GC content, mappability, etc), in one package instead of …
get the uniprot accession from ensembl protein ID
written 10.8 years ago by Moses

Hi, I have a list of Ensembl protein pairs(homologs) with their respective ensembl protein IDs. I want to find a way to convert these Ensembl …
How to visualize a list of genes on their chromosomal position?
written 11.2 years ago by Egon Willighagen

If you go to Ensembl, I can see the location of a gene in the genome browser at various levels. One of these levels is …
Functional Annotation Clustering On The Basis Of Go Terms
written 13.1 years ago by figo

Hi All I have 1000 of human ensemble protein ids and I want to do a functional annotation clustering using Gene ontology (GO) . Can …
Biomart To Go Ontology Terms Using R
written 13.4 years ago by APJ •

Hi, I want to get all the related ensembl gene ids for Gene Ontology term "mouse Embryonic development" . I know to get the Ids …