[maker-devel] does MAKER modify input FASTA

[Carson Holt]

The output fasta will be letter for letter identical to the input fasta
and will be all uppercase.  Only if your input fasta contains unrecognized
characters (for example 'Y' in the middle of the nucleotide sequence) and
you use the --fix_nucleotides flag will those unrecognized characters be
changed to 'N'.  The masked fasta can be pulled out of theVoid directory
if you really need it.  It will be called query_masked.fasta.

--Carson


On 8/13/14, 3:30 AM, "Anurag Priyam" <a.priyam at qmul.ac.uk> wrote:

>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
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org