[galaxy-user] Map with Bowtie for Illumina (version 1.1.2)

2011-10-27 Thread KNIGHT M.R.
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 i

Re: [galaxy-user] Map with Bowtie for Illumina (version 1.1.2)

2011-10-27 Thread Dannon Baker
Hi Marc, 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):" -Dannon On Oct 27, 2011, at 8:40 AM, KNIGHT M.R. wrote: > Hi, is it possible to run Map with Bowtie for Illumin

[galaxy-user] Map with Bowtie for Illumina (version 1.1.2)

2011-10-27 Thread KNIGHT M.R.
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, Director, Durham Centre for Crop Improvement Technology, School of Biological and Biomedical Sciences, Durh