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bedtools Compute both the depth and breadth of coverage (version 2.30.0+galaxy1)

File A (on which coverage is calculated):

BAM/BED/bedGraph/GFF/VCF/EncodePeak format

Combined or separate output files:

File B (for which coverage is calculated):

BAM/BED/bedGraph/GFF/VCF/EncodePeak format

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.

Force strandedness:

Only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand

Report the depth at each position in each A feature:

Positions reported are one based. Each position and depth follow the complete B feature

Report a histogram of coverage for each feature in A as well as a summary histogram for all features in A:

Additional columns after each feature in A: 1) depth 2) # bases at depth 3) size of A 4) % of A at depth

Mean depth:

Report the mean depth of all positions in each A feature.

Minimum overlap required as a fraction of A:

Default is 1E-9, i.e. 1bp.

Minimum overlap required as a fraction of B:

Default is 1E-9, i.e. 1bp.

Require that the fraction overlap be reciprocal for A AND B.:

if -f is 0.90 and -r is used, this requires that B overlap 90% of A and A _also_ overlaps 90% of B

Require that the minimum fraction be satisfied for A OR B.:

If -e is used with -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of B is covered. Without -e, both fractions would have to be satisfied

For coordinate sorted input file the more efficient sweeping algorithm is enabled.:

What it does

bedtools coverage computes both the depth and breadth of coverage of features in file B on the features in file A. For example, bedtools coverage can compute the coverage of sequence alignments (file B) across 1 kilobase (arbitrary) windows (file A) tiling a genome of interest. One advantage that bedtools coverage offers is that it not only counts the number of features that overlap an interval in file A, it also computes the fraction of bases in the interval in A that were overlapped by one or more features. Thus, bedtools coverage also computes the breadth of coverage for each interval in A.

The lines in the output will be comprised of each interval in A, followed by:

The number of features in B that overlapped (by at least one base pair) the A interval.
The number of bases in A that had non-zero coverage from features in B.
The length of the entry in A.
The fraction of bases in A that had non-zero coverage from features in B.

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