length_filter {FastqCleaner}R Documentation

Filter sequences of a FASTQ file by length

Description

The program removes from a ShortReadQ object those sequences with a length lower than rm.min or/and higher than rm.max

Usage

length_filter(input, rm.min = NA, rm.max = NA)

Arguments

input

ShortReadQ object

rm.min

Threshold value for the minimun number of bases

rm.max

Threshold value for the maximum number of bases

Value

Filtered ShortReadQ object

Author(s)

Leandro Roser learoser@gmail.com

Examples

require('Biostrings')
require('ShortRead')

# create  ShortReadQ object width widths between 1 and 100
 
 set.seed(10)
input <- random_length(100, widths = 1:100)

# apply the filter, removing sequences length < 10 or length > 80
filtered <- length_filter(input, rm.min = 10, rm.max = 80)

# look at the filtered sequences
sread(filtered)

[Package FastqCleaner version 1.8.0 Index]