Has anyone been able to build a bowtie index with the mirBase hairpin.fa file? I'm having some weird issues and I don't really know what the story is. I've been able to build other indexes without issue, but the mirbase hairpin file is acting strange. When I try to do an alignment it is not finding the vast majority of alignments with the index. It only finds a small percentage, and these are overwhelming GC-rich with 1 or 2 mismatches. There are no errors in the index building process, although I was a bit confused with one aspect of the build - during the build process this was part of the output:
fchr[A]: 0
fchr[C]: 416893
fchr[G]: 781895
fchr[T]: 1191858
fchr[$]: 1191858
I'd be lying if I said I knew exactly what it meant, but it does seem a bit odd...
Anyone make this index successfully?
PS-miRBase is now on version 17, but I couldn't get this to work with version 16 either
fchr[A]: 0
fchr[C]: 416893
fchr[G]: 781895
fchr[T]: 1191858
fchr[$]: 1191858
I'd be lying if I said I knew exactly what it meant, but it does seem a bit odd...
Anyone make this index successfully?
PS-miRBase is now on version 17, but I couldn't get this to work with version 16 either
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