noPattern

Assess whether a contig/chunk does not have an elevated/gapped read coverage pattern.
A horizontal line at the mean or median coverage should be the best
match if the contig/chunk read coverage is not gapped or elevated.

internal

Automate the detection of gaps and elevations in mapped sequencing
read coverage using a 2D pattern-matching algorithm. 'ProActive' detects, characterizes
and visualizes read coverage patterns in both genomes and metagenomes. Optionally,
users may provide gene annotations associated with their genome or metagenome
in the form of a .gff file. In this case, 'ProActive' will generate an additional
output table containing the gene annotations found within the detected regions of gapped
and elevated read coverage. Additionally, users can search for gene
annotations of interest in the output read coverage plots.

Jessie Maier

ProActive

Detect Elevations and Gaps in Mapped Sequencing Read Coverage

Manuel Kleiner

noPattern function

<dl><dt>pileupSubset</dt>
<dd>A subset of the read coverage dataset that pertains only to
the contig currently being assessed</dd></dl>

Arguments

No read coverage pattern — noPattern

<dl>

<dt>pileupSubset</dt>
<dd>A subset of the read coverage dataset that pertains only to
the contig currently being assessed</dd>

</dl>

noPattern: No read coverage pattern

Description

Usage

Arguments