[mira_talk] Re: cleaning reads

  • From: Jose Blanca <jblanca@xxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Tue, 10 May 2011 08:51:33 +0200

El 09/05/11 17:34, Tony Travis escribió:

On 09/05/11 14:04, Jose Blanca wrote:



lucy is doing quality trims for illumina or only the vector? I'd like to
know about that, because we're not using lucy for quality trimming of
small sequences.


Yikes!! You've reminded me that "lucy" has a default 'good' minimum
sequence length of 100bp, which is not suitable for ~50bp reads. My
"lucy" job would have rejected all the reads ;-)

I've started the job again using a minimum Solexa read-length of 20bp,
which is the default used by MIRA for Solexa reads, I also set the
multiple thread option (-xtra 16) this time to speed things up:


lucy -xtra 16 -minimum 20 MIRA/meta_in.solexa.fasta
MIRA/meta_in.solexa.fasta.qual -vector pCC1BAC.fasta
pCC1BAC-splice.fasta -output MIRA/meta_in.solexa.fasta.screen
MIRA/meta_in.solexa.fasta.qual.screen


Well, AFAIK, "lucy" quality trims reads by default and will reject any
reads shorter than the minimum (default = 100bp) i.e. after trimming.
Have you checked the results? Is lucy cleaning the reads OK? I would think that for this short sequences besides the minimum length filter you wold have to revise also the bracket and window parameters. 
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)

--
You have received this mail because you are subscribed to the mira_talk mailing 
list. For information on how to subscribe or unsubscribe, please visit 
http://www.chevreux.org/mira_mailinglists.html

Other related posts:

  1. Home
  2. mira_talk
  3. Archive
  4. 05-2011