[mira_talk] Re: mira an assembly combiner?
- From: Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 7 May 2013 16:36:37 +0100
On Tue, May 7, 2013 at 4:12 PM, Stephen LeGrande <stlegrande@xxxxxxxxx> wrote:
> If the mapping assemblies have the same reference backbones, I would
> probably try the following:
> Export all sample specific assemblies into SAM/BAM format.
The way MIRA handles the reference/consensus may prevent that.
At the very least, MIRA will insert gaps into the reference, so you'd
need to run 'samtools depad' before merging.
> Aattach sample
> specific labels to the reads of each assembly and merge the individual
> assemblies to a common one by SAMtools or Picard.
I'd use the read groups for this - but MIRA's default IDs would need to
be disambiguated when merging the files.
Peter
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