question about gff to gtf conversion

Question

[Synanth]

Hi,

I am attempting to convert a gff file to gtf for downstream uses. The gff was automatically populated from EDTA, and I have tried gffread, produces blank output, and AGAT, which gives me a series of errors, which look like the following:

gff3 reader warning: primary_tag error @ ltr_retrotransposon still not taken into account! Please modify the json files to define the feature in one of the levels.
gff3 reader warning: primary_tag error @ mutator_tir_transposon still not taken into account! Please modify the json files to define the feature in one of the levels.

There are a large series of these messages, and it looks like the solution, generally, is to edit some files so that AGAT knows how to automatically parse the tags-- however: I do not know how to determine which tag should act as the parent. I'm pretty new to this, so if someone could provide some literature elucidating determination of feature levels-- I would be greatly appreciative.

Best, Synanth

Answer 1

[Juke34]

Specific EDTA feature types (ltr_retrotransposon, mutator_tir_transposon) have been added in most recent version of AGAT. You could either install the version from the master branch or modify yourself the json files as made here (for level2): https://github.com/NBISweden/AGAT/blob/master/share/features_level2.json

[Synanth]

Thank you so much, I was working with the latest version-- but there was a case difference in the names between the two.