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Old 01-27-2012, 01:34 PM   #1
thondeboer
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Default 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
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Old 03-20-2012, 12:36 AM   #2
louis7781x
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Default

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
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Old 09-04-2013, 11:55 PM   #3
sunny.ECNU
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wonderful explaination.Thanks guy from Taipei.
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