(This article was first published on

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

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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