[mira_talk] Re: denovo assembly of genome with a lot of indels
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 18 Oct 2012 00:29:29 +0200
On Oct 17, 2012, at 15:40 , AYeroslaviz wrote:
> we have a PE experiment of mouse genome with loads of mutations in the
> sequence. a bowtie and/or tophat brought only ~2% mapping results. So we
> decided to go with a denovo assembly to see what happens.
>
> That problem is that we are also expecting very large deletions to be found.
> Those are the size of several kb long (we saw traces of them in the tophat
> results, but with a very low read number).
In de-novo assemblies, insertions/deletions play no role as the assembler will
not know what "the reference" should be ... it just cares about what the data
tells it.
> What will happens to inserts bigger than the given distance of 750? will they
> be ignored completely?
You mean, when the library produces many pairs outside the expected
distribution? MIRA will then use one of the reads. If the other is "saved" by
aligning to another contig, so much the better. Else the non-placed mate will
go to debris.
B.
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