[mira_talk] Re: cleaning reads
- From: Tony Travis <a.travis@xxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 09 May 2011 11:24:41 +0100
On 09/05/11 09:44, Jose Blanca wrote:
[...]
Would MIRA
need any additional functionality in clean_reads to work ok?
The clean_reads page is:
http://bioinf.comav.upv.es/clean_reads/
I'll have a look at it as soon as possible, but that may still be in a couple
of weeks only.
As said above: as long as the 454 lowercase/uppercase convention is repscted,
I do not think additional things are required.
We have added a new option to clean_reads in the new clean_reads version
to enable the lowercasing of the regions to be trimmed. We hope you find
it useful.
Hi, Jose.
I installed "clean_reads" 0.1.0 after you posted your message here, but
I've not yet been able to get the parallel version working. The
single-thread version works properly, but is extremely slow cleaning
20x10^6 Solexa reads on a 2GHz Opteron with 64GiB RAM under Bio-Linux 6
(64-bit Ubuntu 10.04). I only managed to clean about 350Mb of a 3.5Gb
Solexa fastq sequence file in 48h, before I aborted the job and tried
the parallel version. What sort of throughput should I normally expect?
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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