Question: Errors in file embl
0
gravatar for kamel
13 days ago by
kamel10
kamel10 wrote:

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

embl file annotation genome • 104 views
ADD COMMENTlink modified 13 days ago by Juke-342.1k • written 13 days ago by kamel10

you can find some pointers in this blog post already : http://avrilomics.blogspot.com/2018/08/converting-gff3-file-to-embl-to-submit.html

ADD REPLYlink modified 13 days ago • written 13 days ago by lieven.sterck4.5k
3
gravatar for Juke-34
13 days ago by
Juke-342.1k
Sweden
Juke-342.1k wrote:

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.

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.

ADD COMMENTlink modified 13 days ago • written 13 days ago by Juke-342.1k

Thank you @jike-34 for your reply. I installed all perl dependencies of GAAS to use your scripts gff3_sp_flag_short_intron.pl. I ran it but it also asks the module "BILS :: CheckModule" but mcpan it can not find this module

ADD REPLYlink modified 12 days ago • written 12 days ago by kamel10

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

ADD REPLYlink modified 12 days ago • written 12 days ago by Juke-342.1k

Thanks @Juke-34 for your help. It is well installed. I have a quick question, Do you think that the argument --translate of EMBLmyGFF3 is mandatory for submission?

ADD REPLYlink modified 10 days ago • written 10 days ago by kamel10

Did you run gff3_sp_flag_short_intron.pl without problem this time ?
No --translate it is not mandatory for submission.

ADD REPLYlink modified 10 days ago • written 10 days ago by Juke-342.1k

Thank you for your reply. Yes I ran gff3_sp_flag_short_intron.pl without any problem. Except sometimes it put twice / pseudo in the same CDS which is not recommended for a valid file, but it works very well. Thanks again.

ADD REPLYlink written 10 days ago by kamel10

I forgot about this duplication of attributes within the EMBL output. Did you find a way to fix it ? Because the validator does not like them... I have fixed that within EMBLmyGFF3 but I didn't push the fix yet...

ADD REPLYlink modified 10 days ago • written 10 days ago by Juke-342.1k

yes the validator found this as an error, unfortunately I delete them manually

ADD REPLYlink written 9 days ago by kamel10

Fix pushed in EMBLmyGFF3 version 1.2.5

ADD REPLYlink written 7 days ago by Juke-342.1k
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