[mira_talk] Re: Lots of long repetitive contigs
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 19 Sep 2012 08:46:48 +0200
On Sep 19, 2012, at 1:55 , Jason Steen wrote:
> I guess I already knew I was going to have a problem. I did use genome mode,
> so I might try est mode and see if its any better.
>
> All I'm really looking for is contigs that relate to the dominant species in
> the metagenome, and then compare that to the sequencing of an isolate from
> that pool. Its one of those projects that sounds easy enough on paper, but
> turns out to be a complete mess once you get started.
>
> Again, thanks for the advice, if I manage to get anything useful, I'll let
> you know
What I would do: if you already know the isolate and you expect the one in the
metagenome to be fairly similar ... why not filtering out (most) reads in the
metagenome which are similar to the ones of your isolate and start from there?
You can use "mirabait" for this: in the first round use your isolate as bait,
then assemble the reads (either de-novo or mapping, mapping would be faster),
then use the result as new bait.
B.
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