Question: StringTie Error regarding GFT file
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gravatar for williamsbrian5064
15 months ago by
williamsbrian5064170 wrote:

Hi,

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.

Thanks!

ADD COMMENTlink modified 13 months ago by Biostar ♦♦ 20 • written 15 months ago by williamsbrian5064170

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 15 months ago by Bastien Hervé4.2k
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