removeDupReads: Remove Sequencing Reads Mapped to Identical Locations
In Rsubread: Mapping, quantification and variant analysis of sequencing data

Description Usage Arguments Details Value Author(s)

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

removeDupReads(

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

`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.

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.

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

Yang Liao and Wei Shi

Rsubread documentation built on March 17, 2021, 6:01 p.m.