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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