MAKER annotation post processing (AED score)

Question

[Picasa]

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

[ricardoguerreiro2121]

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

Answer 1

[dfajar2]

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