Convertion Of Gff3 To Gtf

Question

[daalsa98]

Hi, I'm trying to use this tool to match genomic regions to the closest gene (rgMatch) https://bitbucket.org/pfurio/rgmatch/src/master/, in order to compute the associations, RGmatch needs the following information:

• A GTF annotation file providing the chromosome positions of all the features to be considered (genes, transcripts and exons). This GTF file should include annotations at exon level, that is, the 3rd column of the GTF must contain "exon" tag.
• List item A BED file containing the regions of interest to be associated to features.

However, I have .GFF3 file, I have already tried to use gffread, but when i try to use rgMatch, with the output of gffread, this happens:

> python3 rgmatch.py -g OE9D.gtf -b 70m.bed -o prueba.txt

I have tried to use bioinfokit toolkit, but when I try to convert my gff3, this happens:

Any help would be appreciated

Answer 1

[lieven.sterck]

you can have a look at the AGAT toolkit AGAT - Another Gff/Gtf Analysis Toolkit , there might be some tool in it that can do this.

[daalsa98]

Oh, thanks!, I'll take a look and see if it works

[Juke34]

Apparently you should use agat_sp_fix_cds_phases.pl first if you need proper phases, but you need the original fasta file used to create this annotation file to do so.
Then use agat_convert_sp_gff2gtf.pl

[daalsa98]

So, it kinda worked, but didnt, I followed your advice, and when I tried to run again rgMatch with the new gtf created by AGAT, this happened:

At the end, in KeyError: 'Oe9_s00819', the weird thing It's there is no scaffold Oe9_s00819 in the new gtf, I don't know what it could be happening.

[Juke34]

Sounds to be a python problem. Maybe your tool is expecting python 2.7 and not python3.

[daalsa98]

I've already tried, it happens the same thing

[Juke34]

The warning are definitely Python problem. For the error you should try to get in touch with the rgMatch developer.

[daalsa98]

I will do it, thanks for everything, you have already helped me a lot, really appreciated;)