Convertion Of Gff3 To Gtf

1

Hi, I'm trying to use this tool to match genomic regions to the closest gene (rgMatch) 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


gtf


gff

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