[mira_talk] Re: cleaning reads
- From: Tony Travis <a.travis@xxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 12 May 2011 11:14:56 +0100
On 10/05/11 11:09, Jose Blanca wrote:
[...]
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.
Hi, Jose.
This is the log from my "lucy" job screening 20x10^6 50bp Solexa
pared-end reads:
Bye,
Tony.
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
Less Useful Chunks Yank (lucy) 1.20p, by Hui-Hsien Chou and Michael Holmes,
with help from Granger, Anna, John and Terry Shea.
Phase 1: Checking the number of input sequences...
21180826 input sequences found.
Phase 2: Reading sequence name, length and position data...
0 empty sequences discarded.
Phase 3: Reading quality values and checking good sequence regions...
21180826 quality sequences read; 3893975 low quality sequences dropped.
Phase 4: 2nd sequences comparsion skipped...
no 2nd sequence file provided.
Phase 5: Locating splice sites...Number of splice sequences: 4
2393751 short or no insert sequences discarded.
Phase 6: Kicking out vector sequences...
6881685 vector sequences discarded.
Phase 7: Producing output sequence and quality files...
8011415 good sequences written in MIRA/meta_in.solexa.fasta.screen and
MIRA/meta_in.solexa.fasta.qual.screen.
--
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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