Having created a set of quantiations in SeqMonk you can choose to export these in a format which would allow them to be imported into other genome browsers (UCSC etc) or systems (IGV etc).
The data is exported in bedGraph format which can easily be converted to bigWig format if you prefer using the free tools availble from UCSC.
To export your data select File > Export Current View > BEDGraph. The tool will ask you for a file name. What you specify is a base name onto which the names of each of the currently visible data stores will be appended. Separate files will be made for each of the currently visible data stores and a file of chromosome sizes will also be saved so that the files can immediately be put though the UCSC bedGraphToBigWig program to convert them into bigWig format.
To try to maximise compatibility between different genome browsers, when you save a bedGraph file from seqmonk the chromosome names will all have "chr" prepended to them and the ordering of chromosomes will be made to be completely alphabetical so the files don't need to be re-sorted before indexing.