I am facing another problem with feature counts. I aligned my paired sequence reads to mm10 genome through HISAT2. I then ran these through stringtie. I then merged all the stringtie files together and called transcriptome. I then merged the transcriptome with a mm10 refseq GTF through StringTie Merge. I am now at the stage of pairing each HISAT2 file towared the merged transcriptome. I dont want to use gene_ID for this as it only gives me code for MSTRG, when in fact I need the actual gene name…
As it said its failed to find the ref_gene_id identifier in column 9 but it is there. Also I have ran this before on another RNA-seq dataset and it worked fine.