Question: Looking for SNPs and indels simultaneously in two genome datasets
gravatar for valwc.soo
4.1 years ago by
United States
valwc.soo0 wrote:

Hi all, 

I am very new to NGS and Galaxy, and I have some very basic questions. My goal is to identify potential SNPs and/or indels in my two genome datasets (Illumina, 150 nt paired-end reads). 

One dataset is a re-sequenced wildtype strain, and the other is a mutant strain. I have tried using Bowtie to align each dataset to the reference genome according to this screencast: . While this method worked fine, I got very confused when I tried to determine whether there is new SNPs that appear specifically in my mutant strain but not in my re-sequenced wildtype strain, and vice versa.

I was wondering if it is possible to align two genome datasets at the same time against a reference genome? Having read more about genome alignment for the past 1 h, I suppose BWA is a better tool than Bowtie? 

Your help is very much appreciated. Thank you! 

- Valerie. 

bwa • 1.1k views
ADD COMMENTlink modified 4.1 years ago by Jennifer Hillman Jackson25k • written 4.1 years ago by valwc.soo0
gravatar for Jennifer Hillman Jackson
4.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:


The basic steps in this tutorial at the public Main Galaxy instance should give you a simplified overview:

It includes a comparison of two different variant detection methods, but there are also others (GATK, etc). The protocol also makes use of BWA (Bowtie does not report indels).

More tutorials and resources can be found at: - see "Shared Data -> Published Pages" - see "Other Tutorials"

Good luck with your project! Jen, Galaxy team

ADD COMMENTlink written 4.1 years ago by Jennifer Hillman Jackson25k
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