[maker-devel] does MAKER modify input FASTA

[Carson Holt]

It will actually be a mixture of hard and soft masking depending on the
class of repeat.

--Carson


On 8/13/14, 9:29 AM, "Daniel Ence" <dence at genetics.utah.edu> wrote:

>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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