Stringtie does not work with NCBI GTF file?

Question

[100dustedclays]

Hi all,

I wanted to rerun my DGE analysis to see if there were any differences between HTseq-count -> edgeR and StringTie-Ballgown.

However, when I tried to run my stringtie command using the same BAM file, I got an error: "Error: no valid ID found for GFF record"

I think I read somewhere that Stringtie only likes Ensembl gtfs, I was wondering if one of you can confirm this. My previous DGE analysis was performed using reference genome from NCBI.

Answer 1

[100dustedclays]

Is there a way to delete this post?

I have found a solution from StringTIe Error: no valid ID found for GFF record

NCBI has an extra line in the gtf file that has an input of transcript_id =="" which stringtie does not like. Removing those lines has fixed the issue.

[Mensur Dlakic]

There is a way to delete posts, but there is no need to do it. Just because you found the solution doesn't mean this stops being a problem for others. Instead, your posted solution will help others when they search the archives with a similar problem.