filter_and_trim: Filter and Trim Sample Sequences

In erictleung/dada2HPCPipe: DADA2 HPC Workflow Wrapper

Description

Filters and trims paired forward and reverse FASTQ files.

Usage

filter_and_trim(samplNames, fnFs, fnRs, outDir, truncLen)

Arguments

samplNames	vector of sample names
fnFs	vector of paths to forward samples
fnRs	vector of paths to reverse samples
outDir	specified directory to output filtered reads
truncLen	a vector with two elements, the first being the truncated length for the forward reads and the second being the truncated length for the reverse reads

Value

new filtered reads put into the filtered/ directory

References

fastqFilter vs fastqPairedFilter vs filterAndTrim https://github.com/benjjneb/dada2/issues/311

Examples

# Setup variables
out_dir <- "output"
trunc_len <- c(225, 175)
ids <- c("s001", "s002")

# Import data
pkg <- "dada2HPCPipe"
dat <- "extdata"
sample1 <- system.file(dat, "s001-GTGCTA.fastq", package = pkg)
sample2 <- system.file(dat, "s002-GTGCTG.fastq", package = pkg)

# Run trim and filter
out <- filter_and_trim(ids, sample1, sample2, out_dir, trunc_len)

erictleung/dada2HPCPipe documentation built on May 10, 2019, 1:19 p.m.