Conversion of bed to bigwig

For me wiggle representation is generally for the coverage, so I'll just compute the coverage first using bedtools utility as genomeCoverageBed –i file.bed -bg –g my.genome > sample.cov, where file.bed can be obtained using bamToBed utility bamToBed -i file.bam > file.bed and then would use bedGraphToBigWig utility for ucsc to convert the coverage file to bigwig, which is better than wig as you can place on the local server and pass the text file containing links of these bigwigs to collaborators etc. for viewing with UCSC and its safe as only you having rights can change the file content. Another option would be using pyicos convert tool as pyicos convert my_experiment.bam my_experiment.wig -f SAM -F variable_wig -O, this will give you wig directly.

Cited from https://www.biostars.org/p/2699/

bedGraphToBigWig is downloadable from http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64.v287/