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,