Thread: BFAST published
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Old 11-20-2009, 03:12 PM   #15
Location: Toronto

Join Date: Nov 2009
Posts: 24

Originally Posted by nilshomer View Post
Absolutely! A similar example is suppose you have prior evidence of RNA splicing between two novel exons in which you only know the approximate boundaries (say within 100bp). You can create all possible joins of the two 100bp windows and then align your reads to the artificial reference to see which join is the most likely.
Thanks a lot for your quick reply, Nils! Could you give me a bit more details about how to do this? I remember in your paper you said when the best alignment of a read map to more than one locations on the reference equally well (in my example would be more than one cDNA sequences, which usually correspond to the same locations on the underlying genome) then you would say the read is not mapped, but I would like BFAST to output all the mappings regardless. I haven't downloaded your tool yet but will do so as soon as I finish the work at hand!
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