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.*

*seths...@comcast.net*

*650 996 8726 (cell)*



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