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,

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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