Enveomics collection

BedGraph.tad.rb

Estimates the truncated average sequencing depth (TAD) from a BedGraph file.

    See source code, Artistic license 2.0.

§ References

    Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.

§ Requirements

• Ruby >= 2.0.

§ Usage

BedGraph.tad.rb --input in_file [opts]

§ Arguments

Input*

 --input in_file  Input BedGraph file. Supports compression with .gz extension, use - for STDIN.

Output

 --output out_file  Output tab-delimited values (by default, STDOUT). Supports compression with .gz extension, use - for STDOUT.

Range

 --range float  Central range to consider, between 0 and 1. By default: inter-quartile range (0.5).

Name

 --name string  Name (ID) of the sequence, added as first column.

Per seq

 --per-seq   Calculate averages per reference sequence, not total. Assumes a sorted BedGraph file.

Length

 --length   Add sequence length to the output.

* Mandatory.