[mira_talk] Re: Assembling 454 and Solexa mate-pair data - rethinking ...
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 16 Sep 2009 22:58:12 +0200
On Dienstag 15 September 2009 Martin A. Hansen wrote:
> I have tried yet another approach for this assembly. I assumed that the
> Solexa data was contaminated, so I ran MIRA with the 454 contigs (used as
> long Sanger reads) and the Solexa mate-pairs - but only the mate pairs that
> could be mapped to the contigs (using Bowtie and allowing for 3
> mismatches). This reduced the amount of mate-pairs from 3M to 1M, and still
> reads should be included that spans the gaps between the contigs.
> [...]
> This strikes me as completely wrong. The long contigs are gone.
> According to the log both Sanger and Solexa reads were loaded (I omitted
> the quals on purpose expecting a simple run).
Ummm ... MIRA did not reject the "reads" longer than 20kb? Then I think did
you turn of all clippings for the "Sanger" reads. Especially if you did not
load quals ... I suspect that the quality clipping algorithms (turned on by
default) threw them out without a second look.
Search the output log for the name of one or two of your fake Sangers ... you
might find them with a messagge saying that thesy don't have enough bases
(after quality clip).
Also have a look at the "*_int_clippings.0.txt" in the log directory ... this
should also tell you what happened to your reads after loading.
Regards,
Bastien
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