gffread outputs empty gtf file

Question

[sumitra.20]

Hi,

I've been trying to convert my prokka output in gff format to gtf format to be able to use for my hisat-stringtie analysis. However, using gffreads to convert yields an empty gtf file. Im not sure if im going wrong somewhere. Any help will be appreciated.

gffread ./b.mega_hybrid.gff -T -o sequence.gtf

Answer 1

[inedraylig]

Do you use excel to view and save the gff file or did you only use it for the question? What is the source of the gff file?

Generally, it's best to avoid graphic editors (Excel, OpenOffice) when working with text-based files like gff. If you do, my advice is to use command-line as much as possible. One of the reasons is that when you save the file in a graphic editor, it will change the contents of the file (add field delimiters and other complicated elements). My guess, in that case, is that Excel did something unexpected to the gff, so that gffread cannot parse it. My other advice is to start by looking at the example files provided with gffread (but do it on command line), that way you may spot the property in your file that causes the problem.