[BioC] total number of reads? mapped reads? or total counts?

[wang peter]

hello all


In the edgeR package，
  the lib.size: vector of length ncol(counts) giving the total number
of reads sequenced
for each sample. If not separately provided, will be set to colSums(counts).

but there are three different concepts.

usually the number of mapped reads < total reads < counts
because not all of the reads can be mapped
and one mapped reads have more than 1 hit.

so which one should be used in the NB model?

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