fixed_filter {FastqCleaner} | R Documentation

## Remove a fixed number of bases of a ShortReadQ object from 3' or 5'

### Description

The program removes a given number of bases from the 3' or 5' regions of the sequences contained in a ShortReadQ object

### Usage

    fixed_filter(input, trim3 = NA, trim5 = NA)

### Arguments

`input` | `ShortReadQ` object
`trim3` | Number of bases to remove from 3'
`trim5` | Number of bases to remove from 5'

### Value

Filtered `ShortReadQ` object

### Author(s)

Leandro Roser learoser@gmail.com

### Examples

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

    # create 6 sequences of width 20

    set.seed(10)
    input <- random_seq(6, 20)

    # create qualities of width 20

    set.seed(10)
    input_q <- random_qual(c(30,40), slength = 6, swidth = 20,
    encod = 'Sanger')

    # create names
    input_names <- seq_names(6)

    # create ShortReadQ object
    my_read <- ShortReadQ(sread = input, quality = input_q, id = input_names)

    # apply the filter
    filtered3 <- fixed_filter(my_read, trim5 = 5)

    filtered5 <- fixed_filter(my_read, trim3 = 5)

    filtered3and5 <- fixed_filter(my_read, trim3 = 10, trim5 = 5)

    # look at the trimmed sequences
    sread(filtered3)
    sread(filtered5)
    sread(filtered3and5)

[Package FastqCleaner version 1.4.0 Index]