On 10/02/2013 12:35 AM, Abhishek Pratap wrote:
> Hi All
> Just wanted to check on the expected behavior of the
> function in the GenomicRanges package for the following cases.
> 1. In the case of paired end data does it count each read pair as 1
> against a feature.
Pairs are counted as a single 'hit' reguardless if one or both mates
overlap the feature.
> 2. For stranded protocols of RNA-Seq does it take it account the
> strand of the mate of a read when counting or does it take only one
> matching the strand into consideration.
When counting, pairs are treated as though they are from the same
strand. In general, you can ignore the strand when counting by setting
> 3. For second strand RNA-Seq protocol where the read-1 matches to
> opposite strand of gene will summarizeOverlap work ?
I'm not sure what you mean. Please provide an example.
summarizeOverlaps() reads the data from a BAM into a GAlignmentPairs
GAlignmentsList container for counting. You can investigate the
using a small test case.
## paired-end record
ga1 <- GAlignments("chr1", 1L, "10M", strand("+"))
ga2 <- GAlignments("chr1", 15L, "11M", strand("-"))
galp <- GAlignmentPairs(ga1, ga2, TRUE)
ann <- GRanges("chr1", IRanges(c(1, 5, 12, 20), c(25, 20, 14, 30)),
## all with mode="Union"
se1 <- summarizeOverlaps(ann, galp, ignore.strand=TRUE)
se2 <- summarizeOverlaps(ann, galp, ignore.strand=FALSE)
se3 <- summarizeOverlaps(ann, galp, ignore.strand=TRUE)
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