removeDupReads {Rsubread} | R Documentation

## Remove Sequencing Reads Mapped to Identical Locations

### Description

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

### Usage

    removeDupReads(

        # basic input/output options
        inputFile,
        threshold = 50,
        outputFile,
        outputFormat = "BAM")

### Arguments

`inputFile` | a character string giving the name of a SAM or BAM 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.
`outputFormat` | a character string giving the format of the output file. `BAM` and `SAM` are accepted. `BAM` by default.

### 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

This function generates a BAM or SAM file including the remaining reads after duplicate removal.

### Author(s)

Yang Liao and Wei Shi

[Package Rsubread version 2.4.3 Index]