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 names. So I decided to use ref_gene_id as the identifier. However, everytime I do this it comes up with an error saying:
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
The specified gene identifier attribute is ‘ref_gene_id’
However, from the images enclosed it can be clearly shown ref_gene_id is mentioned in the 9th column alongside gene_id and transcript_id. I’m really stuck and dont know what to do from this. I have previously used ref_gene_id on another RNA-seq experiment and it worked fine.