Hi biostar,
Maybe basic questions but I can not solve this problem. I wanted to validate an embl file. After the validation I find two errors (below)
ERROR: Intron is usually expected to be at least 10 nt long ERROR: Abutting features can not be adjacent between neighboring exons.
Have an idea about how I could fix one or both errors.
Thank you
1 answer
For the intron size problem, you can fix that by adding the /pseudo attribute. Have a look here to understand the meaning of this attribute.
If you want I have a script that do it automatically.
It is called gff3_sp_flag_short_intron.pl and you can find it in the GAAS repository.
It is called agat_sp_flag_short_introns.pl and is part of the of GFF toolkit AGAT.
For this Abutting features error, if the two features are from different genes then it is a bug from their validator. Have a look here. They advise to remove the exons from the flat file to avoid that type of problem. Otherwise you have to modify location manually.
It just mean that you haven't completed the installation procedure.
Everything starting by BILS is related to a personal library that is within the GAAS repo.
To access them (because it is not the only one needed) 2 choices:
cd GAAS
make install
source profiles/activate_env
or add in your ~/.bashrc or ~/.profile file (provide the correct path):
export PERL5LIB=$PERL5LIB:/pathTo/GAAS/annotation export
PATH=${PATH}:/pathTo/GAAS/annotation/Tools/bin
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you can find some pointers in this blog post already : http://avrilomics.blogspot.com/2018/08/converting-gff3-file-to-embl-to-submit.html