[mira_talk] Re: cleaning reads
- From: Jose Blanca <jblanca@xxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 09 May 2011 12:40:27 +0200
El 09/05/11 12:24, Tony Travis escribió:
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.
What problem do you have? To be able to use several threads you have to
install a python library called psubprocess that you can find also in
our web site. Have you psubprocess installed?
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?
I don't know, that will depend a lot on the type of analysis that you're
doing. For example, if you provide an adaptor file a blast for every
read will be carried out. If you also provide a vector file another
blast will be done, etc. Usually we use several threads to speed up the
process.
Best regards,
Jose Blanca
Bye,
Tony.
--
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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