Calculates genome coverage using bedtools genomecov.

Element type: genomecov

Parameters

ParameterDescriptionDefault valueParameter in Workflow FileType
Output directorySelect an output directory. Custom - specify the output directory in the 'Custom directory' parameter. Workflow - internal workflow directory. Input file - the directory of the input file.Input fileout-modenumeric
Custom directory

Specify the output directory.


custom-dirstring
Output file nameA name of an output file. If default of empty value is provided the output name is the name of the first file with additional extention.
out-namestring
GenomeIn order to prevent the extension of intervals beyond chromosome boundaries, bedtools slop requires a genome file defining the length of each chromosome or contig (-g).human.hg18genomestring
Report mode

Histogram () - Compute a histogram of coverage.

Per-base (0-based) (-dz) - Compute the depth of feature coverage for each base on each chromosome (0-based).

Per-base (1-based) (-d) - Compute the depth of feature coverage for each base on each chromosome (1-based)

BEDGRAPH (-bg) - Produces genome-wide coverage output in BEDGRAPH format.

BEDGRAPH (including uncoveded) (-bga) - Produces genome-wide coverage output in BEDGRAPH format (including uncovered). 

Histogrammode-idnumeric
SplitTreat “split” BAM or BED12 entries as distinct BED intervals when computing coverage. For BAM files, this uses the CIGAR “N” and “D” operations to infer the blocks for computing coverage. For BED12 files, this uses the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12) (-split).Falsesplit-idboolean
StrandCalculate coverage of intervals from a specific strand. With BED files, requires at least 6 columns (strand is column 6) (-strand).Falsestrand-idboolean

5 prime

Calculate coverage of 5’ positions (instead of entire interval) (-5).Falseprime5-idboolean
3 primeCalculate coverage of 3’ positions (instead of entire interval) (-3).Falseprime3-idboolean
MaxCombine all positions with a depth >= max into a single bin in the histogram (-max).2147483647max-idnumeric
ScaleScale the coverage by a constant factor.Each coverage value is multiplied by this factor before being reported. Useful for normalizing coverage by, e.g., reads per million (RPM). Default is 1.0; i.e., unscaled (-scale).1.00000scale-idnumeric
TracklineAdds a UCSC/Genome-Browser track line definition in the first line of the output (-trackline).Falsetrackline-idboolean
TrackoptsWrites additional track line definition parameters in the first line (-trackopts).
trackopts-idstring

Input/Output Ports

The element has 1 input port:

Name in GUI: Input File

Name in Workflow File: in-file

Slots:

Slot In GUISlot in Workflow FileType
Source URLurlstring

And 1 output port:

Name in GUI: Output File

Name in Workflow File: out-file

Slots:

Slot In GUISlot in Workflow FileType
Source URLurlstring