Does anyone know how to do spliced alignment (i.e. with N's in the CIGAR string) on colour-space data with BWA? I've had no luck even with -e 100000 -O 2 -E 0: I don't get a single spliced alignment with those options. I've also tried a trial version of NovoalignCS but it crashes and haven't heard back from their developers. TopHat doesn't do colour-space. So basically I'm struggling to do intron-skipping gapped alignment on colour-space data at the moment... Any help would be appreciated.
Thanks.
Thanks.
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