Galaxy |

bedtools Genome Coverage (version 2.30.0)

Input type:

BED/bedGraph/GFF/VCF/EncodePeak file:

Genome file:

Output type:

Report regions with zero coverage:

If set, regions without any coverage will also be reported

Scale the coverage by a constant factor:

Each bedGraph coverage value is multiplied by this factor before being reported. Useful for normalizing coverage by, e.g., reads per million (RPM).

Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage.:

If set, the coverage will be calculated based the spliced intervals only. For BAM files, this inspects the CIGAR N operation to infer the blocks for computing coverage. For BED12 files, this inspects the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12). If this option is not set, coverage will be calculated based on the interval's START/END coordinates, and would include introns in the case of RNAseq data.

Calculate coverage based on:

Report the depth at each genome position with 1-based coordinates:

Report the depth at each genome position with 0-based coordinatess:

Calculate coverage of 5’ positions:

Instead of entire interval

Calculate coverage of 3’ positions:

Instead of entire interval

What it does

This tool calculates the genome-wide coverage of intervals defined in a BAM or BED file and reports them in BedGraph format.

The input BED or BAM file must be sorted by chromosome name (but doesn't necessarily have to be sorted by start position).

Example 1

Input (BED format)- Overlapping, un-sorted intervals:

chr1    140 176
chr1    100 130
chr1    120 147

Output (BedGraph format)- Sorted, non-overlapping intervals, with coverage value on the 4th column:

chr1    100 120 1
chr1    120 130 2
chr1    130 140 1
chr1    140 147 2
chr1    147 176 1

Example 2 - with ZERO-Regions selected (assuming hg19)

Input (BED format)- Overlapping, un-sorted intervals:

chr1    140 176
chr1    100 130
chr1    120 147

BedGraph output will contain five columns:

Chromosome name (or 'genome' for whole-genome coverage)

Coverage depth

The number of bases on chromosome (or genome) with depth equal to column 2.

The size of chromosome (or entire genome) in base pairs

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.

Citation

If you use this tool in Galaxy, please cite:

Bjoern A. Gruening (2014), Galaxy wrapper