coverage(), form Views() on the coverage for your genes and then viewSums().

On Fri, Jul 22, 2011 at 2:36 PM, Kunbin Qu <KQu@genomichealth.com> wrote:

> Hi,
>
> If I want to count the coverage base by base, not read by read, can I still
> use countOverlaps? I have a human transcriptome done, and would like to
> count the coverage for each gene based on the mapping. As there are some
> reads mapped across the junctions (ie, one read is splitted into two
> portions), or partially mapped into the introns, it would be good to count
> the coverage by base pair, instead of by read number? Could anybody suggest
> a way doing that? Thanks.
>
> -Kunbin
>
>
>
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