I'd like to add to the general cookbook. If some bioc people out there can contribute some alignment recipes can fill me in on some more basics please comment:
alignedReads <- readAligned("./", pattern="output.bowtie", type="Bowtie")
#how many reads did I attempt to align
#i don't think you can't get this from alignedReads
#how many reads aligned (one or more times)
length(unique(id(alignedReads)))
#how many hits were there?
length(alignedReads)
#how many reads produced multiple hits
length(unique(id(alignedReads[srduplicated(id(alignedReads))])))
#how many reads produced multiple hits at the best strata?
#please fill me in on this one
#how many reads aligned uniquely (with exactly one hit)
length(unique(id(alignedReads)))-length(unique(id(alignedReads[srduplicated(id(alignedReads))])))
#how many reads aligned uniquely at the best strata (the other hits were not as good)
#please fill me in on this one
#how many unique positions were hit? what if I ignore strand?
#please fill me in on this one
#how many converging hits were there (two query sequences aligned to the same genomic position)
#please fill me in on this one
put this on biostar. let's see how it does:
ReplyDeletehttp://biostar.stackexchange.com/questions/735/how-do-i-get-some-basic-counts-from-readaligned