pybedtools.contrib.bigwig.bam_to_bigwig

pybedtools.contrib.bigwig.bam_to_bigwig(bam, genome, output, scale=False)

Given a BAM file bam and assembly genome, create a bigWig file scaled such that the values represent scaled reads – that is, reads per million mapped reads.

(Disable this scaling step with scale=False; in this case values will indicate number of reads)

Assumes that bedGraphToBigWig from UCSC tools is installed; see http://genome.ucsc.edu/goldenPath/help/bigWig.html for more details on the format.