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Question: Can Tophat Take Snps Into Account?
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gravatar for Hoang, Thanh
5.2 years ago by
Hoang, Thanh • 200
Hoang, Thanh • 200 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
rna-seq tophat • 976 views
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modified 5.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 5.2 years ago by Hoang, Thanh • 200
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gravatar for Jennifer Hillman Jackson
5.2 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hello Thanh, 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. Best, Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org
ADD COMMENT • link written 5.2 years ago by Jennifer Hillman Jackson ♦ 25k
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