[maker-devel] Extract FASTA Sequences from "Maker Standard" Build

[Jason Gallant]

Hi Everyone,

Quick question— I’ve run through Mike Cambell’s tutorial on building “Maker
Standard”, “Maker Default” and “Maker Max” datasets.  I’ve decided that the
“Maker Standard” data (Transcripts with Evidence and/or IPR scan hits)
makes the most sense for what we’re trying to do.

Is there an easy way to create the fasta files associated with the maker
standard build?  Fasta_merge typically outputs a variety of .fasta files,
which I’ve been able to create following this protocol for the “maker max”
dataset.  I’d like to get these for the “maker standard” build.

Currently, the datastore contains the data for the “maker max” data.  One
way, i suppose would be to re-run MAKER with the maker standard gff file,
but it seems like an overly complicated way of doing it…?

Any suggestions Mike (or others?)  Has anyone written a script to do this
automagically?

Best,
Jason Gallant
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