"Error parsing strand (?) from GFF line" happenning in gffread, stringtie and cufflinks

Question

[Guilherme]

Hi!

I'm working with various genomic data and while trying to use gffread, stringtie and cufflinks I went through the same error:

Error parsing strand (?) from GFF line: NC_037304.1 RefSeq gene 58315 59481 . ? . ID=gene-DA397_mgp34;Dbxref=GeneID:36335702;Name=nad1;exception=trans-splicing;gbkey=Gene;gene=nad1;gene_biotype=protein_coding;locus_tag=DA397_mgp34;part=2 

I recognize this is a formatting error from the GFF file (in this case I'm showing the one from TAIR 10), but it happened in various species. From what I read in this discussion, " '?' can be used for features whose strandedness is relevant, but unknown.". If that's the case, shouldn't these programs recognize the '?' character? More importantly, how can I pass through that? Would it be just by trying to find other annotations? I'd find that odd, because of the fact that the TAIR 10 genome is really well-known for its quality, so I'd doubt that their gff file has such a simple mistake...

Thank you!

[Pierre Lindenbaum]

cross posted: https://stackoverflow.com/questions/75251639

Answer 1

[Shiyi]

write a Rscript to replace the ? with . will get you through right now. then feed into gffread

[Guilherme]

Wouldn't I lose information doing that?

Answer 2

[hafiz.talhamalik]

I am facing the same issue in stringtie. Any solution ??