pileupFormatter

Place columns in correct order, clean accessions by removing text after white
space, and name columns

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

pileupFormatter function

<dl><dt>pileup</dt>
<dd>A .txt file containing mapped sequencing read coverages averaged over
100 bp windows/bins.</dd>
<dt>mode</dt>
<dd>Either "genome" or "metagenome"</dd></dl>

Arguments

Reformat input pileup file — pileupFormatter

<dl>

<dt>pileup</dt>
<dd>A .txt file containing mapped sequencing read coverages averaged over
100 bp windows/bins.</dd>


<dt>mode</dt>
<dd>Either "genome" or "metagenome"</dd>

</dl>

pileupFormatter: Reformat input pileup file

Description

Usage

Arguments