Question: Using EnsDb.Hsapiens.v86 database doesn't fetch the ENSEMBL IDs
gravatar for sutturka
7 weeks ago by
sutturka0 wrote:

Recently I noticed that using the database annotated specific genes (e.g. CASC15, ACTR3BP5, STAG3L3) with ENSEMBL IDs as "NA". This could be the limitation of database.

I tried EnsDb.Hsapiens.v86 which could determine the correct ENSEMBL IDs for these features.


edb <- EnsDb.Hsapiens.v86
transcripts(edb, filter = GeneNameFilter("CASC15"))

I was able to use the same database in ChIPSeeker without any issues but somehow it does not captured the ENSEMBL ID which is available in the column named gene_id.


Anno <- annotatePeak(bedfile, tssRegion=c(-3000, 3000), TxDb=TxDb.Hsapiens.UCSC.hg38.knownGene, annoDb=EnsDb.Hsapiens.v86)

This fetched the annotation columns "geneId", "transcriptId", "distanceToTSS", "SYMBOL", "GENENAME". How to modify the ChIPSeeker code to get the column "gene_id" from the EnsDb.Hsapiens.v86 database?


chipseeker • 101 views
ADD COMMENTlink written 7 weeks ago by sutturka0

annotatePeak is hard-coded to look for geneId, not gene_id - see here:

You may want to create an issue on the GitHub page, and/or literally edit the column name of the object EnsDb.Hsapiens.v86

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by Kevin Blighe340
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 312 users visited in the last hour