How to change stringtie gene_id names with ref_gene_id when performing featureCount
Entering edit mode
Last seen 5.5 years ago

Hi everybody!

I would like to know if there is a way to change stringtie "geneid" with "refgene_id" when performing featureCount to construct the count table for edgeR.

The thing is that I have use stringtie to create a merged gtf file, using all the files I want to compare in the DEG analysis. After that I have use featureCount to create the count matrix, and as featureCount uses gtf file "geneid" by default, in the result count table, I have a very big list of MSTRG------ named genes. I would like to know if using an option in featureCount gives the posibility to change from geneid to refgeneid that is the ENSMBLE ID.

Maybe -g < string > (GTF.attrType), option and ther use "refgeneid"? Would this change be correct? Or maybe I have realized now that there is another option named −−extraAttributes < string > (GTF.attrType.extra) and I can add there refgeneid?

Thanks in advance,


featureCount rna-seq gene_id re_gene_id stringtie • 1.9k views
Entering edit mode
Wei Shi ★ 3.6k
Last seen 5 weeks ago
Australia/Melbourne/Olivia Newton-John …

If "refgeneid" is included as an attribute type in your GTF file, you can set GTF.attrType="refgeneid" to instruct featureCounts to count reads to this type of genes.

The parameter "GTF.attrType.extra" does not work for this purpose. It just extracts extra annotation data from your gtf file and adds them to featureCounts output.


Login before adding your answer.

Traffic: 639 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