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/
***
  

 

 

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