So, I ran Stringtie on data derived from 38 samples, according to the protocol mentioned in the paper - https://www.nature.com/articles/nprot.2016.095. I generated the merged gtf file after running
stringtie merge (using the -G option), and then I performed transcript abundance calculation.
After that, I used the method given here to run tximport using the Stringtie files. However, upon doing that, I saw that tximport just gave one large number for each sample, instead of raw counts for each gene. So, I tried to look at the data carefully and found that there was no gene_names in the stringtie_merged gtf file, as a result of which (probably) tximport wasn't able to give separate counts for the genes/transcripts. (In comparison, the merged.gtf file in their paper does have gene_names at least for some transcripts)
Then, I searched online and found a code by the developer here that is supposed to append gene_names to the merged.gtf file, but on using it, the output gtf still doesn't have any gene names.
TLDR - what should I do to ensure that the merged.gtf file has the gene_names so that tximport can assign raw counts to the transcripts/genes?