Hi Seth,

If the goal is to go forward with variant detection (SAMTools, GATK, etc.) , then you will want to use BWA.

There is also an amplicon-specific mapper in the Tool Shed, if you want to try it out. Do a search using "amplicon" to locate it. Using the tool would require a local or cloud Galaxy instance.
http://toolshed.g2.bx.psu.edu
http://getgalaxy.org
http://usegalaxy.org/cloud

Best,

Jen
Galaxy team

On 7/17/13 9:25 AM, Seth Stern wrote:

Hi Everyone,

I’ve got an amplicon that has fixed and variable sequence segments, and Im sequencing it with 180 base MiSeq reads. I’d like to align the reads using the fixed segment. Is this an appropriate job for either Bowtie or BWA (using a reference sequence that is necessarily shorter than the reads) ? If not, how should I do it ?

Thanks,

Seth

Seth Stern, Ph.D.

sethster@comcast.net

650 996 8726 (cell)
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/

-- 
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org