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Old 01-27-2012, 02:34 PM   #1
Location: Bay Area

Join Date: Jan 2009
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Default Anyone know how Snowshoes-FTD finds junction-spanning reads?


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?


Thon de Boer, Ph.D.
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Old 03-20-2012, 01:36 AM   #2
Location: Hong Kong

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

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 09-05-2013, 12:55 AM   #3
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Location: Shanghai,East China Normal Universtiy

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wonderful explaination.Thanks guy from Taipei.
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gene fusion, rna-seq

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