Can Rsubread output use Ensembl gene IDs
Entering edit mode
Last seen 23 months ago
Cleveland, OH

I am using Rsubread to analyze human FASTQ files from the ENA. I downloaded a GRCh38 FASTA from ENCODE to create and index. I used the featureCounts(bam.files, annot.inbuilt = "hg38") function to count mapped reads for genomic features. Everything seems to work fine, but the count matrices are annotated to Entrez IDs, and I want the output using Ensembl IDs. Is there a way to do that?


Ensembl Rsubread • 938 views
Entering edit mode
Last seen 4 hours ago
WEHI, Melbourne, Australia

The Rsubread inbuilt annotation is RefSeq rather than Ensembl for the reasons explained here:

But featureCounts works with any annotation. If you want Ensembl IDs, then input the Ensembl GTF file to featureCounts using annot.ext instead of annot.inbuilt. See help("featureCounts").

Note that this is not merely a matter of annotating the count matrix. If you use different gene annotation, then the whole count matrix will change so as to correspond to the genes and exons in the new annotation file.


Login before adding your answer.

Traffic: 554 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6