Both, thanks a lot for your help.  I understand the problems inherent in
dealing with this, I was just asking how it is currently handled.  I
suggest expanding the relevant section in the vignette, giving some more
detail, but perhaps I am the only one wondering about this.

I ended up doing a fair amount by hand myself, so I was in control.  I was
actually surprised to learn that the mapping settings had a dramatic effect
on the results (going from 1500 DE peaks to 5000 DE peaks) and to some
extent the overlapping calculation as well.  Is this something you have
investigated?

Best,
Kasper


On Tue, Jun 18, 2013 at 10:51 AM, Gordon Brown
<Gordon.Brown@cruk.cam.ac.uk>wrote:

> Hi, Rory, Kasper,
>
> DiffBind's original counting code treats paired-end data the same as
> single-end, i.e. each read is considered separately, with no attention
> paid to whether it's part of a pair.  As long as all the libraries are the
> same (all S.E. or all P.E.) it shouldn't affect the outcome; counts will
> just be double for P.E. cases (disregarding improperly paired reads).
>
> To fix it properly, since we accept bed as well as bam, we'd have to test
> for properly paired reads ourselves, possibly doing it just that bit
> differently from other tools.  Personally, I'd rather not open that box...
>
> Cheers,
>
>  - Gord
>
>
> On 2013-06-17 23:55, "Rory Stark" <Rory.Stark@cruk.cam.ac.uk> wrote:
>
> >Hi Kasper-
> >
> >From 1.6 on, if the bLowMem parameter is set to TRUE in dba.count,
> >DiffBind will use summarizeOverlaps. Changing the config value
> >DBA$config$singleEnd to FALSE allows it to use paired-end BAM files. The
> >documentation for summarizeOverlaps in the GenomicRanges
> > package explains how it handles paired-end data.
> >
> >Gord, how does the default count code handle paired-end data (in pre-1.6
> >DiffBind, or when bLowMem=FALSE)?
> >
> >Cheers-
> >Rory
> >
> >________________________________________
> >From: Kasper Daniel Hansen [kasperdanielhansen@gmail.com]
> >Sent: 17 June 2013 21:51
> >To: Rory Stark
> >Subject: diffbind, paired end reads
> >
> >
> >Hi Rory
> >
> >
> >Just skimming DiffBind.  I was surprised there is not a longer discussion
> >of dba.count() in the vignette regarding supported input formats.  I also
> >read (skimmed) the man pages.  It is not clear to me if DiffBind supports
> >paired end reads in the counting
> > step (and also how it deals with for example a paired end read where
> >only one mate aligns).
> >
> >
> >Hope all is well in Cambridge.
> >
> >
> >Best,
> >Kasper
>
>

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