removeDupReads: Remove sequencing reads which are mapped to identical...

Description Usage Arguments Details Value Author(s)

View source: R/removeDupReads.R

Description

Remove reads which are mapped to identical locations, using mapping location of the first base of each read.

Usage

1
removeDupReads(SAMfile,threshold=50,outputFile)

Arguments

SAMfile

a character string giving the name of a SAM format input file.

threshold

a numeric value giving the threshold for removing duplicated reads, 50 by default. Reads will be removed if they are found to be duplicated equal to or more than threshold times.

outputFile

a character string giving the base name of output files.

Details

This function uses the mapping location of first base of each read to find duplicated reads. Reads are removed if they are duplicated more than threshold number of times.

Value

A SAM file including the remaining reads after duplicate removal.

Author(s)

Yang Liao and Wei Shi


Bioconductor-mirror/Rsubread documentation built on July 14, 2017, 8:49 a.m.