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
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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