pybedtools.contrib.bigwig.bam_to_bigwig¶
-
pybedtools.contrib.bigwig.
bam_to_bigwig
(bam, genome, output, scale=False)[source]¶ Given a BAM file
bam
and assemblygenome
, 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.