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

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!

cufflinks gff gffread stringtie
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updated by hafiz.talhamalik hafiz.talhamalik • written by Guilherme • Guilherme

2 answers

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

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written by Shiyi • Shiyi

Wouldn't I lose information doing that?

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written by Guilherme • Guilherme

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

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written by hafiz.talhamalik hafiz.talhamalik

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