I have been mapping my RNA-seq data to mouse genome from a different
strain using TopHat. I am wondering whether TopHat can take SNPs into
account during the alignment? ( using SNPs track as an optional
To my knowledge, a base substitution will be noted, but an insertion
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
using a custom reference genome, you can set-up TopHat2 on your local
cloud with appropriate indexes there.
More is in the documentation for each tool - review the latest
the tool-specific support groups is highly recommended to see what
others are doing currently and to find out about any known issues.