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I obtained stringtie 2.2.1 through apt-get and there is a possibility this has been fixed in later versions, however I did not find it in the releasenotes.
Stringtie does not seem to be able to parse strands with value "?". GFF spec allows this.
Error parsing strand (?) from GFF line:
NC_042756.1 RefSeq mRNA 119185 219853 . ? . ID=rna-FKU89_mgp27;Parent=gene-FKU89_mgp27;Dbxref=GeneID:40498719;exception=trans-splicing;gbkey=mRNA;gene=nad5;locus_tag=FKU89_mgp27
The reference file was obtained from https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon=4236 and provided to stringtie using -G option
Thank you for maintaining this tool, I use it often
Edit: upon further investigation, the same happens in version 3.0.0 obtained from github
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