It would seem that you can't create issues on a forked repository, so I'm creating this one here. Sorry.
Anyway - a user has kindly been looking into the results that we sent them as they seemed a little strange. Only two miRBase hits were reported. When she ran a similar alignment against some other data with known miRNAs in it, the same two hits were reported (only). After some digging she realised that the miRBase reference sequences are encoded as RNA; using U instead of T. Two sequences from bizarre species are the exception, and those were the two hits that we were returning.
So, the miRBase reference needs to be converted to DNA before alignments are generated. Then we should get a few more hits!
It would seem that you can't create issues on a forked repository, so I'm creating this one here. Sorry.
Anyway - a user has kindly been looking into the results that we sent them as they seemed a little strange. Only two miRBase hits were reported. When she ran a similar alignment against some other data with known miRNAs in it, the same two hits were reported (only). After some digging she realised that the miRBase reference sequences are encoded as RNA; using
Uinstead ofT. Two sequences from bizarre species are the exception, and those were the two hits that we were returning.So, the miRBase reference needs to be converted to DNA before alignments are generated. Then we should get a few more hits!