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Calculates genome coverage using bedtools genomecov.

Parameters in GUI

ParameterDescriptionDefault value
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 file
Custom directory

Specify the output directory.

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. 
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.hg18
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). 

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).False
StrandCalculate coverage of intervals from a specific strand. With BED files, requires at least 6 columns (strand is column 6) (-strand).False

5 prime

Calculate coverage of 5’ positions (instead of entire interval) (-5).False
3 primeCalculate coverage of 3’ positions (instead of entire interval) (-3).False
MaxCombine all positions with a depth >= max into a single bin in the histogram (-max).2147483647
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).1.00000
TracklineAdds a UCSC/Genome-Browser track line definition in the first line of the output (-trackline).False
TrackoptsWrites additional track line definition parameters in the first line (-trackopts). 

Parameters in Workflow File 

Type: genomecov

ParameterParameter in the GUIType
out-modeOutput directorynumeric
custom-dirCustom directorystring
out-nameOutput file namestring
genome Genomestring
mode-idReport modenumeric
prime5-id5 primeboolean
prime3-id3 primeboolean

Input/Output Ports

The element has 1 input port:

Name in GUI: Input File

Name in Workflow File: in-file


Slot In GUISlot in Workflow FileType
Source URLurlstring

And 1 output port:

Name in GUI: Output File

Name in Workflow File: out-file


Slot In GUISlot in Workflow FileType
Source URLurlstring
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