genomeChunks

Subset genome pileup into chunks for pattern-matching

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

genomeChunks function

<dl><dt>pileup</dt>
<dd>A .txt file containing mapped sequencing read coverages averaged over
100 bp windows/bins.</dd>
<dt>chunkSize</dt>
<dd>If `mode`="genome" OR if `mode`="metagenome" and `chunkContigs`=TRUE,
chunk the genome or contigs, respectively, into smaller subsets for pattern-matching.
`chunkSize` determines the size (in bp) of each 'chunk'. Default is 50000.</dd></dl>

Arguments

'chunk' genomes — genomeChunks

<dl>

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


<dt>chunkSize</dt>
<dd>If `mode`="genome" OR if `mode`="metagenome" and `chunkContigs`=TRUE,
chunk the genome or contigs, respectively, into smaller subsets for pattern-matching.
`chunkSize` determines the size (in bp) of each 'chunk'. Default is 50000.</dd>

</dl>

genomeChunks: 'chunk' genomes

Description

Usage

Arguments