22 months ago by
CRUK, Cambridge, UK
DiffBind sets the minimum read count for consensus peaks to 1. Basically, this avoids divide-by-zero checking etc. One-read differences shouldn't make a difference in meaningful results (although it does skew the read distribution).
bFullLibrarySize option determines the total read count used for normalization. If
bFullLibrarySize=FALSE, the number of reads that overlap consensus peaks is used for each sample (basically, the sum of all the counts). This is the best option for cases where most of the peaks are not expected to change their binding affinity significantly. For the more conservative default,
bFullLibrarySize=TRUE, the total number of aligned reads in the .bam file is used (basically the sequencing depth). This is more appropriate in cases where you expect dramatic shifts in binding affinities, or if you are not sure what to expect.
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