[mira_talk] Re: Correct 454 errors with Solexa reads?
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 16 Dec 2009 22:55:19 +0100
On Montag 14 Dezember 2009 Björn Nystedt wrote:
> mapping Solexa with MIRA to a fasta backbone
Quick and dirty ... but already very effective when investing ~0.5 to 1 hour
per MB in editing the result of this: use different strain names for the FASTA
backbone and the Solexa reads, then search for SROc, WRMc, UNSc and IUPc.
Eventually MCVc.
> mapping Solexa with MIRA to a caf backbone
A bit slower, not by much. You might need to invest a bit more time in
editing, but the full hybrid appoach allows you to see what caused the 454
error.
> de-novo assembly with MIRA, using all data (including fake 20kb overlapping
> reads to avoid messing up the original assembly) (slow!) mapping Solexa
> with another software BWA/SOAP2/RMAP/Bowtie to a fasta backbone de-novo
> assembly with Velvet, using all data (not so slow)
No idea. Can you put the Velvet result into a finishing program?
> So far we have run the mapping in MIRA to a fasta backbone, wich works
> quite nice but not perfectly (see previous discussion on the list
> 'Alignment errors in Solexa mapping').
I think every mapper will have the same problems. If not, I need to rethink a
few things :-)
Regards,
Bastien
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