length_filter: Filter sequences of a FASTQ file by length

In FastqCleaner: A Shiny Application for Quality Control, Filtering and Trimming of FASTQ Files

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 [e-mail]

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)

FastqCleaner documentation built on Nov. 8, 2020, 5:05 p.m.