Function pairs aligned paired NGS reads

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Description

This function takes bowtie output files, pairs the reads, only keeps those where both ends mapped, filters for perfect duplicates to avoid PCR bias, and saves and returns a GenomicRangesList object that contains the paired_reads_1 and paired_reads_2 GenomicRanges with the paired reads

Usage

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pairReads(fileName1, fileName2, sampleName, DUPLICATETHRESHOLD = 1,
fileType='BAM')

Arguments

fileName1

File containing the mapped reads of the first fragment ends (BAM or Bowtie format)

fileName2

File containing the mapped reads of the second fragment ends (BAM or Bowtie format)

sampleName

A character string that will be used to name the exported BedGraph file containing the coverage, and the R object file with paired reads. They will be saved in the current directory.

DUPLICATETHRESHOLD

An integer specifying the maximum amount of duplicated paired-end reads allowed, over that value it is expected to be PCR bias. The default is 1.

fileType

A character string specifying the format of the aligned reads. The default is 'BAM'. Other accepted format is 'Bowtie'.

Value

A GenomicRangesList called filtered

paired_reads_1

GenomicRanges with the coordinates of where one end of the read mapped

paired_reads_2

GenomicRanges with the coordinates of where the other end of the read mapped

Author(s)

Borbala Mifsud and Robert Sugar

See Also

mapReadsToRestrictionSites, GOTHiC

Examples

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library(GOTHiC)
dirPath <- system.file("extdata", package="HiCDataLymphoblast")
fileName1 <- list.files(dirPath, full.names=TRUE)[1]
fileName2 <- list.files(dirPath, full.names=TRUE)[2]
paired <- pairReads(fileName1, fileName2, sampleName='lymphoid_chr20', 
DUPLICATETHRESHOLD = 1, fileType='Table')