Yes, if you change "Bowtie settings to use" from common to full, you'll see the entire parameter list, including "Number of mismatches for SOAP-like alignment policy (-v):"
On Oct 27, 2011, at 8:40 AM, KNIGHT M.R. wrote:
> Hi, is it possible to run Map with Bowtie for Illumina (version 1.1.2) in –v alignment mode/ If so, what settings do I need to enter? Many thanks, Marc.
> Professor Marc R. Knight,
> Durham Centre for Crop Improvement Technology,
> School of Biological and Biomedical Sciences,
> Durham University,
> South Road,
> Durham DH1 3LE.
> Tel: +44 191 33 41224
> Fax: +44 191 33 41201
> Website: http://www.dur.ac.uk/dccit/ > ***
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Hi, I’m trying to assemble Illumina paired sequence which is at least 15x deep to the Arabidopsis genome (TAIR 10 version) using Map with Bowtie for Illumina (version 1.1.2) but try as I might with changing all the parameters in different ways to reduce stringency I am still getting a lot of gaps in the assembly (probably about 10% missing). What settings would you advise I focus on to try and improve the situation? Many thanks in advance! Marc.
*** Professor Marc R. Knight, Director,
Durham Centre for Crop Improvement Technology,
School of Biological and Biomedical Sciences, Durham University, South Road, Durham DH1 3LE. Tel: +44 191 33 41224 Fax: +44 191 33 41201 Website: http://www.dur.ac.uk/dccit/ ***