trimFastq: Trim the fastq files

In ge11232002/NGS: Next Generation Sequencing Data Analysis

Description

Given the argument of trimLeft, trimRight and minTailQuality, this function trims the fastq files and generate the new files.

Usage

  trimFastq(reads1, outputDir=".", paired=TRUE, nReads=-1L, 
            minTailQuality=20, trimLeft=0L, trimRight=0L,
            mc.cores=getThreads())

Arguments

reads1	The character vector. The filenames of first reads.
outputDir	When to save the trimmed fastq files.
paired	Whether paired-end reads or single-end reads.
nReads	Only sample a certain number nReads of reads. By default, all reads will be processed.
minTailQuality	The minimal tail quaility to decided where to cut. We use a runnning windows of size 4 to calculate the quality at each base, and cut off the tail at the first base where the quality is below minTailQuality. By default, it is 20. If the length of the trimmed read is below half of original read, this read is discarded.
trimLeft	The number of bases to cut on the left of the read.
trimRight	The number of bases to cut on the right (tail) of the read.
mc.cores	The number of threads to use. By default, we use a internal function NGS:::getThreads to decide.

Value

The filenames of trimmed first reads are returned.

Author(s)

Ge Tan

Examples

  reads1 <- file.path(system.file("extdata", package="NGS"), "fastq", 
                      "nanocage_ACAGAT_carp_embryo_R1.fastq")
  trimmedFastqs <- trimFastq(reads1, outputDir=".", paired=TRUE, 
                             nReads=-1L, 
                             minTailQuality=20, 
                             trimLeft=0L, trimRight=0L,
                             mc.cores=1L)
  file.remove(trimmedFastqs, NGS:::getPairedReads(trimmedFastqs))

ge11232002/NGS documentation built on May 17, 2019, 12:13 a.m.