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

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

[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 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,
> Durham University,
> South Road,
> Durham DH1 3LE.
> Tel: +44 191 33 41224
> Fax: +44 191 33 41201
> Website: http://www.dur.ac.uk/dccit/
> ***
>  
>  
>  
> ___
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
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> use the Galaxy Development list:
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> please use the interface at:
> 
>  http://lists.bx.psu.edu/


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

[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,
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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[galaxy-user] Map with Bowtie for Illumina

[Sonali Thakur]

Hello,

We are getting below error with the Map with Bowtie for
Illuminatool.
Please suggest.

Traceback (most recent call last):
  File "/var/www/galaxy/lib/galaxy/jobs/runners/local.py", line 55, in
run_job
job_wrapper.prepare()
  File "/var/www/galaxy/lib/galaxy/jobs/__init__.py", line 347, in prepare
self.command_line = self.tool.build_command_line( param_dict )
  File "/var/www/galaxy/lib/galaxy/tools/__init__.py", line 1515, in
build_command_line
command_line = fill_template( self.command, context=param_dict )
  File "/var/www/galaxy/lib/galaxy/util/template.py", line 9, in
fill_template
return str( Template( source=template_text, searchList=[context] ) )
  File
"/var/www/galaxy/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg/Cheetah/Template.py",
line 1004, in __str__
return getattr(self, mainMethName)()
  File "DynamicallyCompiledCheetahTemplate.py", line 222, in respond
IndexError: list index out of range

Thanks
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