To my knowledge, a base substitution will be noted, but an insertion or deletion will be missed. BWA is a better tool for this if DNA, and TopHat2 if RNA (use a custom reference genome if on the pubic server). As NGS Jobs are not running on the public instance right now, instead of using a custom reference genome, you can set-up TopHat2 on your local or cloud with appropriate indexes there.
More is in the documentation for each tool - review the latest including the tool-specific support groups is highly recommended to see what others are doing currently and to find out about any known issues.
Jen Galaxy team
On 10/2/13 6:55 PM, Hoang, Thanh wrote:
Hi, I have been mapping my RNA-seq data to mouse genome from a different mouse strain using TopHat. I am wondering whether TopHat can take SNPs into account during the alignment? ( using SNPs track as an optional input)? Thanks Thanh
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