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-   -   Anyone know how Snowshoes-FTD finds junction-spanning reads? (http://seqanswers.com/forums/showthread.php?t=17179)

thondeboer 01-27-2012 01:34 PM

Anyone know how Snowshoes-FTD finds junction-spanning reads?
 
Hi,

I am trying to figure out how the gene fusion program Snowshoes-FTD finds junction spanning reads. I have the article from NAR, but it does not mention how this is done. In Figure 1, it simply states that it aligns the not-mapped reads (not mapped with BWA to either genome or their special exon-exon junction DB) to both fusion partners.

This seems to be the most important part of a gene fusion procedure, since this will actually get you the breakpoint, but the paper does not seem to discuss at all how it does this. I assume some dynamic programming algorithm, but I can't tell.

I don't have access to the program, since it is not freely available so maybe someone here knows?

Thanks

Thon

louis7781x 03-20-2012 12:36 AM

First,
It used discordant paired-end to find fusion candidates.
Example: |---geneA---|----------------------|---geneB---|

Second,
All unmapped reads from genome and exon-exon boundary will use megablast to align geneA and geneB to find exact break point span within geneA and geneB

sunny.ECNU 09-04-2013 11:55 PM

wonderful explaination.Thanks guy from Taipei.


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