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: http://screencast.g2.bx.psu.edu/galaxy/quickie12_illumina_pe/flow.html . 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!