One possibility is that you need to use ignore.strand = TRUE in your
subsetByOverlaps call, i.e., you are filtering out all of those negative
strand reads.

Michael

On Fri, Mar 9, 2012 at 9:29 AM, Lakshmanan Iyer <laxvid@gmail.com> wrote:

> I am calculating the coverage on a subset of a gapped aliment that obtained
> using "subsetByOverlaps" between a "GappedAlignments" and a "GRanges"
> object
> #> class (Dendaligns)
> #[1] "GappedAlignments"
> #attr(,"package")
> #[1] "GenomicRanges"
> #> class (p3UTRsChr)
> #[1] "GRanges"
> #attr(,"package")
> #[1] "GenomicRanges"
> DendfiltData2 <- subsetByOverlaps (Dendaligns, p3UTRsChr);
> #> class (DendfiltData2)
> #[1] "GappedAlignments"
> #attr(,"package")
> #[1] "GenomicRanges"
> #
> # Find coverage
> Dendcov <- coverage(DendfiltData2)
> #
> # Find islands of coverage with min value of 1
> Dendislands <- slice (Dendcov, lower=1);
> #
> # convert the island ranges in to a data frame
> DendislandsData <- as.data.frame (ranges(Dendislands[[chr]]) );
> #
> # extract the scores of the coverage in a list
> Dendisland_scores <- viewApply (Dendislands[[chr]], function (x)
> as.integer(x))
>
> When I look at the scores, the first island contains a series of 1 (45 of
> them in my case).
> However, when I visualize the same regions in IGV with the raw bam file
> (see attached picture), I see that the counts are > 1 for bases after first
> 10 bases.
>
> I am wondering where the counting becomes different from summing up the
> reads at any position!
>
> Thanks for any thoughts
> -best
> -Lax
>
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