Question: StringTie Error regarding GFT file
gravatar for williamsbrian5064
2.3 years ago by
williamsbrian5064250 wrote:


I am working on some RNA seq data. A colleague of mind inserted a human gene into the Drosophila genome. I'm trying to figure out how to add the gene to the fasta file and the gtf file so I can see the expression of the gene. Do anyone know how to do that? I attempted to add the gene to the fasta file and I think it worked because I didn't get any errors. I am struggling with the gtf file I keep getting an error that StringTie is getting this error

"Error parsing attribute transcript_id (' " ' required) at GTF line: xxxxxxxxx

The xxxxxxxxx line being where I attempted to instead the human gene in the gtf file. Does anyone know how to insert a gene into a GTF file? I am clearly doing something wrong here.


ADD COMMENTlink modified 2.1 years ago by Biostar ♦♦ 20 • written 2.3 years ago by williamsbrian5064250

If you could share with us the line you try to insert that would be helpful. And the context of insertion (2 or 3 lines before insertion and 2 or 3 line after). Just copy/paste these 5 lines at the end of your question. Thanks

Seems like you do not have a transcript_id in the inserted line.

ADD REPLYlink written 2.3 years ago by Bastien Hervé4.5k
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