[mira_talk] Re: gff to gff3

  • From: Bastien Chevreux <bach@xxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Thu, 23 Oct 2014 11:05:25 +0200 (CEST)

On October 23, 2014 at 10:25 AM Andrej Benjak <abenjak@xxxxxxxxx> wrote:

> To use a gff file as reference in MIRA make sure the nucleotide sequence is
> embedded in the file, then it should work.
>  (most gff files out there, including those from NCBI, don't contain any
> sequence)
> 

Albeit if the GFF3 does not have the sequence embedded, you can load it from a
separate file (like the data you get from the NCBI). E.g.:

readgroup
...
data= somefile.fnadata = somefile.gff3

You just need to take care that the sequence file really is the one belonging to
the GFF3 file. MIRA can catch a number of mix-up cases, but not all. Therefore,
GFF3 with sequence embedded is my recommended approach.

B.

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