bedGraph Handling

bedGraph is a text format for displaying continuous-valued data on genome browsers. Common for coverage, signal intensity, and scores.

bedGraph Format

track type=bedGraph name="Sample" description="Coverage"
chr1    0       100     1.5
chr1    100     200     2.3
chr1    200     300     0.8

Four columns: chrom, start, end, value (0-based, half-open)

Create bedGraph from BAM

Using bedtools genomecov