Hi Parvati,
Your GTF file does not have “gene” in column3 and “gene_name” in Attributes. Use values present in the GTF file.
Kind regards,
Igor
Hi Igor,
Thank you, I retried featurecounts using the valid values, I have mRNA in my column 3 which is what I am interested in, Hence I used it as GFF feature type filter. And I do have gene_name in my 9th column but it still fails to recognize it.
I also tried using ID as an identifier, but it does not give me any hits,
I would be needing the gene names for my further analysis. Could you please help on how I can get featurecounts to recognise the attribute gene_name?
Best,
Parvati.
Try converting your GFF3 file to GTF format with gffread again.
Something didn’t go right the first time if I am looking at the correct screenshots you posted. It looks like the file was converted to a GFF format of some type. That won’t work – set the output type on the tool form to GTF specifically. Until that conversion is done correctly, Featurecounts is unlikely to work how you want it to.
How this is done can impact the scientific meaning of the results, even if the tool doesn’t fail. That means Igor’s advice to use GTF to start with is very good – so, please try that again. Leave the Featurecounts tool form settings at the default values since those are for a GTF already.
Later on, once you get the basic way this tool is used working correctly, you can experiment on your own more. We have quite a bit of discussion at this forum you can explore. 