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 1.6.0 Index]