Error parsing attribute transcript_id (" " required)

Question

[Yuyayuya]

Hello everyone,

I was using StringTie to get gene count and I got the error message:

After checking, I found the difference between reference.GTF file I used and standard is the " " sign for gene_id and transxript_id.

Here's the format of the .GTF file I used:

I didn't get error when I used another .GTF file. Here's how it looks:

Is this error due to " " issue?
If yes, does anyone happen to know how to solve it?

Thanks in advance!

Answer 1

[Renesh]

GFF parser code in StringTie expects double quotes around the textual attributes and that's why you are getting this error. You can use the gffread utility to validate your gff files and convert your files into the correct format.

GFF utilities can be found here http://ccb.jhu.edu/software/stringtie/gff.shtml

[Yuyayuya]

Thank you! It works!

Answer 2

[Yuyayuya]

Thank you!! It works.