(This article was first published on

The UCR guide is a little sparse with regard to getting basic information from readAligned.**Jermdemo Raised to the Law**, and kindly contributed to R-bloggers)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

To

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