highlightAssemblyErrors: highlightAssemblyErrors - Master function to identify...

In oneillkza/ContiBAIT: Improves Early Build Genome Assemblies using Strand-Seq Data

Description

highlightAssemblyErrors – Master function to identify misorientations and chimeras in the assembly

Usage

highlightAssemblyErrors(path, splitBy = 1e+06, cluster = 1,
  clusterParam = NULL, pairedEnd = TRUE, qual = 10, gapFile = NULL,
  verbose = TRUE)

Arguments

path	String denoting location of Strand-seq bam files
splitBy	integer determining the average size contigs should be split by
cluster	Number of times to recluster and take the consensus of. If NULL, clustering is run only once.
clusterParam	optional BiocParallelParam specifying cluster to use for parallel execution. When NULL, execution will be serial.
pairedEnd	Whether the bam files being read are in paired end format. Default is TRUE. Note,
qual	Mapping quality threshold. Default is 1
gapFile	A GRanges object consisting of start and end locations of assembly gaps (defaul it NULL)
verbose	prints messages to the terminal (default is TRUE)

Value

a directional ChrTable object that can be used in downstream functions (strandSeqFreqTable)

oneillkza/ContiBAIT documentation built on June 1, 2020, 5:49 a.m.