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Question: Amplicon Sequencing Questions
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gravatar for Seth Stern
5.4 years ago by
Seth Stern • 40
Seth Stern • 40 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)
bwa alignment bowtie • 1.2k views
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modified 4.4 years ago by Lena.Rueschstroer • 0 • written 5.4 years ago by Seth Stern • 40
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gravatar for Jennifer Hillman Jackson
5.4 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
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 -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org
ADD COMMENT • link written 5.4 years ago by Jennifer Hillman Jackson ♦ 25k
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gravatar for Lena.Rueschstroer
4.4 years ago by
Lena.Rueschstroer • 0
Germany
Lena.Rueschstroer • 0 wrote:

Hi,

I tried to find the amplicon- specific mapper in the Tool Shed, but I was not able to find it. Is it still available and if yes how is it exactly called?

Thanks,

Lena
ADD COMMENT • link written 4.4 years ago by Lena.Rueschstroer • 0
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