[nilshomer]

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!

By default, BFAST outputs all mappings for a read regardless of their quality/score. It is only in the postprocessing step do we use various criteria (specified by the user) to choose the "best" alignment. One of those criteria is to output all alignments, which is what you want.

[HTS]

By default, BFAST outputs all mappings for a read regardless of their quality/score. It is only in the postprocessing step do we use various criteria (specified by the user) to choose the "best" alignment. One of those criteria is to output all alignments, which is what you want.

Great, thanks a lot! I can't wait to try things out!