Question: MAKER annotation post processing (AED score)
3
gravatar for Picasa
3.3 years ago by
Picasa560
Picasa560 wrote:

Hi,

I have successfully annotated my genome with MAKER. Now I have a gff file that I want to post process /filter.

In particular, I would like to discard gene that is below a certain AED score.

1) Is there an AED treshold from where a gene is not strongly supported ? if yes, do you have some reference about this ?

2) Is there a script/software to process a gff file ?

Thanks

maker aed • 4.2k views
ADD COMMENTlink modified 3.1 years ago by dfajar290 • written 3.3 years ago by Picasa560

The first question has not been answered yet. I'd like knowing. I'm right now filtering on 0.5 AED score.

ADD REPLYlink written 4 weeks ago by ricardoguerreiro212160
3
gravatar for dfajar2
3.1 years ago by
dfajar290
dfajar290 wrote:

You should go through this document, it is really useful. http://www.yandell-lab.org/publications/pdf/maker_current_protocols.pdf

Also, you can find the quality_filter.pl script here https://groups.google.com/forum/#!searchin/maker-devel/quality_filter.pl%7Csort:relevance/maker-devel/LC4STWWlwgo/XV4nhGiHsfIJ

You can filter based on AED and/or interproscan evidence.

$ perl ~/scripts/quality_filter.pl

quality_filter.pl: generates defualt and standard gene builds from a maker geneated gff3_file with iprscan data pushed onto column 9 using ipr_update_gff.

USAGE: quality_filter.pl -[options]<gff3_file>

OPTIONS: -d Prints transcripts with an AED <1 (MAKER default) -s Prints transcripts with an AED <1 and/or Pfam domain if in gff3 (MAKER Standard) -a <number between="" 0="" and="" 1=""> Prints transcripts with an AED < the given value

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by dfajar290
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1272 users visited in the last hour