Is it possible to normalize a coverage plot made by AlignmnetsTrack( file.bam) by the library size? I tried to use transform function in plotTracks( ), but it doesn't change the AlignmentsTrack coverage output.

Hi,

You did not provide any code. It is hard to guess where the problem could be. 

Typical mistake is not using full argument name. You need to provide the transformation function as argument called "transformation". The name has to be exact. For example this works for me:

library(Gviz)
afrom <- 2960000
ato <- 3160000
alTrackOrig <- AlignmentsTrack(system.file(package="Gviz", "extdata", "gapped.bam"), isPaired=TRUE, type="coverage")
alTrackTransformed <- AlignmentsTrack(system.file(package="Gviz", "extdata", "gapped.bam"), isPaired=TRUE, 
                           transformation=function(x) {x*10}, type="coverage")
plotTracks(list(alTrackOrig, alTrackTransformed), from=afrom, to=ato, chromosome="chr12")