[mira_talk] Re: MIRA assembly - Geneious 8 - extra IUPAC codes
- From: Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Mon, 22 Dec 2014 12:59:32 +0000
On Mon, Dec 22, 2014 at 12:49 PM, Zain A Alvi <zain.alvi@xxxxxxxxxxxxxxx> wrote:
> Hi Everyone,
>
> I was able to run MIRA this past weekend on the workstation
> (Geneious) with no problems. Thank you everyone for the help.
>
> There is one small problem that I am having is with the output.
> The output is very specific and includes R, Y, S, K, and other
> IUPAC codes for the nucleotide sequences. I was wondering
> if there is a method to make MIRA to not include ambiguities
> in the alignment results. I hope to run a BLASTX based on
> the genome assembly from MIRA. These IUPAC codes
> makes BLASTX think that I am working with an amino acid
> sequences instead of nucleotide sequence.
This is covered in the fine manual, and is important for any
downstream tools which fail to handle IUPAC codes:
http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html
> Also does MIRA like interleaved/interlaced files for paired end
> alignment or the paired end reads to be just separate like with
> some other assemblers like
Either, MIRA uses the read names rather than the order in the file(s).
Peter
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