Brief description of the deeptools-bamcoverage program:
This tool takes an alignment of reads or fragments as input (BAM file) and
generates a coverage track (bigWig or bedGraph) as output. The coverage is
calculated as the number of reads per bin, where bins are short consecutive
counting windows of a defined size. It is possible to extended the length of
the reads to better reflect the actual fragment length. bamCoverage offers
normalization by scaling factor, Reads Per Kilobase per Million mapped reads
(RPKM), and 1x depth (reads per genome coverage, RPGC).
Brief description of the deeptools-bamcoverage program: