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Create a histogram of genome coverage (version 0.1.0)
Combine all positions with a depth >= max into a single bin in the histogram.

What it does

This tool calculates a histogram of genome coverage depth based on mapped reads in BAM format or intervals in BED format.

This tool requires that bedtools has been installed on your system.

The output file will contain five columns:

    1. Chromosome name (or 'genome' for whole-genome coverage)
    1. Coverage depth
    1. The number of bases on chromosome (or genome) with depth equal to column 2.
    1. The size of chromosome (or entire genome) in base pairs
    1. The fraction of bases on chromosome (or entire genome) with depth equal to column 2.

Example Output:

chr2L       0           1379895     23011544    0.0599653
chr2L       1           837250      23011544    0.0363839
chr2L       2           904442      23011544    0.0393038
chr2L       3           913723      23011544    0.0397072
chr2L       4           952166      23011544    0.0413778
chr2L       5           967763      23011544    0.0420555
chr2L       6           986331      23011544    0.0428624
chr2L       7           998244      23011544    0.0433801
chr2L       8           995791      23011544    0.0432735
chr2L       9           996398      23011544    0.0432999

This tool is part of the bedtools package from the Quinlan laboratory. If you use this tool, please cite Quinlan AR, and Hall I.M. BEDTools: A flexible framework for comparing genomic features. Bioinformatics, 2010, 26, 6.