parse_fastq_eestats2: Load USEARCH fastq_eestats2 report

In vmikk/metagMisc: Miscellaneous functions for metagenomic analysis

Load USEARCH fastq_eestats2 report

Description

Load USEARCH fastq_eestats2 report showing how many reads will pass an expected error filter at different length thresholds.

Usage

parse_fastq_eestats2(file, long = FALSE)

Arguments

file	the name of the input file.
long	a logical value indicating wheather the results should be returned in long format.

Details

This function depends on plyr and reshape2 packages. Additional details on 'fastq_eestats2' function can be found on http://drive5.com/usearch/manual/cmd_fastq_eestats2.html

Value

data frame

Examples

## Run USEARCH
# usearch -fastq_eestats2 reads.fq -output eestats2.txt -length_cutoffs 200,300,10
parse_fastq_eestats2("eestats2.txt", long = F)
parse_fastq_eestats2("eestats2.txt", long = T)

library(ggplot2)
ee <- parse_fastq_eestats2("eestats2.txt", long = T)
ggplot(data = ee, aes(x = Length, y = NumberOfReads, group = MaxEE, color = as.factor(MaxEE))) + 
  geom_point(size = 2) + 
  geom_line() + 
  theme_classic()

vmikk/metagMisc documentation built on Feb. 14, 2024, 2:29 a.m.