[mira_talk] Re: cleaning reads
- From: Jose Blanca <jblanca@xxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 10 May 2011 12:09:48 +0200
El 10/05/11 11:31, Tony Travis escribió:
On 10/05/11 07:51, Jose Blanca wrote:
[...]
Hi, Jose.
Yes, I've checked the results on a subset of the data - I'm interested
in using "lucy" to screen vector out, and relying on the two default
windows (50 and 10 bases) to match vector. I've previously used the
"cross_match" program from Phred/Phrap to vector screen, or "ssaha2".
I'd be grateful for your advice about optimal "lucy" parameters to
screen 50bp Solexa reads, even if that means use "clean_reads" ;-)
We did some tests and we didn't manage to clean such sort reads. I would
like to know which are those optimal lucy parameters for the short reads
by the lucy manual I didn't manage to understand which ones would be the
best. Due to this problem we do not use lucy to clean the short illumina
and solid reads, we use a simple sliding window algorithm programed in
clean_reads.
Best regards,
--
Jose M. Blanca Postigo
Instituto Universitario de Conservacion y
Mejora de la Agrodiversidad Valenciana (COMAV)
Universidad Politecnica de Valencia (UPV)
Edificio CPI (Ciudad Politecnica de la Innovacion), 8E
46022 Valencia (SPAIN)
Tlf.:+34-96-3877000 (ext 88473)
--
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