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.
On 10/2/13 6:55 PM, Hoang, Thanh wrote:
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
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