[mira_talk] Re: cleaning reads
- From: Tony Travis <a.travis@xxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 09 May 2011 16:34:57 +0100
On 09/05/11 14:04, Jose Blanca wrote:
[...]
Send me the clean_reads.error file please. We do not have a bug tracker
yet because we have few users.
Hi, Jose.
OK, I've done that.
it has done 18x10^6 of the reads in 12h:
lucy meta_in.solexa.fasta meta_in.solexa.fasta.qual -vector
pCC1BAC.fasta pCC1BAC-splice.fasta -output meta_in.solexa.fasta.screen
meta_in.solexa.fasta.qual.scree
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.
Bye,
Tony.
--
Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk
mailto:a.travis@xxxxxxxxxx, http://bioinformatics.rri.sari.ac.uk
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