[maker-devel] does MAKER modify input FASTA

[Daniel Ence]

Hi Priyam, 

After MAKER has completed it's run and you've merged the results with gff3_merge, you can see the original fasta genome in the resulting gff3 file, below the ##FASTA pragma. 

For each scaffold in your genome, the masked fasta can be found in it's individual directory in the master_datastore that MAKER created to keep track of results. I'm pretty sure this will only be 'soft-masked' (lower-case letters) and not hard-masked ('N' characters). 

Let me know whether this helps, 
Daniel


Daniel Ence
Graduate Student
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
________________________________________
From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of Anurag Priyam [a.priyam at qmul.ac.uk]
Sent: Wednesday, August 13, 2014 3:30 AM
To: maker-devel at yandell-lab.org
Subject: [maker-devel] does MAKER modify input FASTA

Is it possible that the input FASTA file (containing the genome that
is being annotated) and the FASTA sequences in the output GFF file
(containing the resulting annotations + the genome) be different?

-> It's fine if the ordering of the scaffolds, or width (for pretty
formatting) are different.
-> But, will MAKER add 'NNN' or change the case to indicate masking?
It doesn't seem so to me, but I have only one test set, so can't be
sure.
-> Is it possible to get masked genome out from MAKER?

-- Priyam

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