XenoFilteR: XenofilteR: excluding host reads from xenograft sequencing...

In PeeperLab/XenofilteR: Excluding host reads from xenograft sequencing data

XenofilteR: excluding host reads from xenograft sequencing data

Description

Excludes DNA or RNA sequence reads that originate from contaminating species (like the host in xenograft experiments.

Usage

XenofilteR(sample.list, destination.folder, bp.param, output.names, MM_threshold, Unmapped_penalty)

Arguments

sample.list	A data.frame or matrix that contains the full name of the bam files (including path) of the reads aligned to the human reference (column 1) and the mouse reference (column 2).
destination.folder	The path to the folder to which output should be written. The path can be either absolute or relative.
bp.param	A BiocParallelParam instance (see BiocParallel Bioconductor package) that determines the settings used for parallel computing. Please refer to the vignette for more information.
output.names	Optional list with alternative samples names for the generated filtered bam file. This might become useful when analysing RNAseq data. Bam files are often name identical and sample names are defined in the folder name, not in he bam file.
MM_threshold	The edit distance of reads that map to the human reference only should be below this threshold. Default = 4.
Unmapped_penalty	Only applicable for paired-end sequence data. If one of the reads of a pair is not mapped the edit distance for that read is set to this value. Default = 8.

Details

XenofilteR reads four parameters from the human and mouse bam file: 1) read name, 2) mapping quality, 3) CIGAR, and 4) mismatches (NM tag). Based on these parameters XenofilteR calculates two edit distances for each read, one for the mapping to the human (graft) reference and a second for the mapping to the mouse (host) reference. The read or read-pair is assigned to the host or graft .bam files based on these edit distances.

Value

BamFiles	A folder with the .bam files from which reads mapping to xenogemones have been removed.
XenofilteR.log	Log file of XenofilteR. This file also contains the statistics for each sample processed.

Author(s)

Oscar Krijgsman ([e-mail]) Roel Kluin ([e-mail])

References

XenofilteR: seperate graft from host reads in xenograft sequencing. Roel Kluin, Oscar Krijgsman, et al. To be submitted for publication.

Examples

## Not run: 
# 
library(XenofilteR)
path <- dir(system.file(package = "XenofilteR"), "extdata", full.names = TRUE)
samples <- list.files(path = path, pattern = ".bam$", full.names = TRUE)

sample.list <- data.frame(samples[1], samples[2])
bp.param <- SnowParam(workers = 1, type = "SOCK")

XenofilteR(sample.list = sample.list, destination.folder =
        "/PATH/TO/DESTINATIONFOLDER/", bp.param = bp.param, output.names = NULL, MM_threshold=4, Unmapped_penalty = 8))

## End(Not run)

PeeperLab/XenofilteR documentation built on July 8, 2022, 11:30 p.m.