fixed_filter: Remove a fixed number of bases of a ShortReadQ object from 3'...

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

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 [e-mail]

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)

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