| trim3q_filter {FastqCleaner} | R Documentation |
The program removes from the 3' tails of the sequences a set of nucleotides showing a quality < a threshold value in a ShortReadQ object
trim3q_filter(input, rm.3qual, q_format = NULL, check.encod = TRUE, remove_zero = TRUE)
input |
|
rm.3qual |
Quality threshold for 3' tails |
q_format |
Quality format used for the file, as returned by check_encoding |
check.encod |
Check the encoding of the sequence? This argument is incompatible with q_format. Default TRUE |
remove_zero |
Remove zero-length sequences? |
Filtered ShortReadQ
object
Leandro Roser learoser@gmail.com
require('Biostrings')
require('ShortRead')
# create 6 sequences of width 20
set.seed(10)
input <- random_seq(6, 20)
# create qualities of width 15 and paste to qualities
# of length 5 used for the tails.
# for two of the sequences, put low qualities in tails
set.seed(10)
my_qual <- random_qual(c(30,40), slength = 6, swidth = 15,
encod = 'Sanger')
set.seed(10)
tails <- random_qual(c(30,40), slength = 6, swidth = 5,
encod = 'Sanger')
set.seed(10)
tails[2:3] <- random_qual(c(3, 20), slength = 2,
swidth = 5, encod = 'Sanger')
my_qual <- paste0(my_qual, tails)
input_q <- BStringSet(my_qual)
# create names
input_names <- seq_names(6)
# create ShortReadQ object
my_read <- ShortReadQ(sread = input,
quality = input_q, id = input_names)
# apply the filter
filtered <- trim3q_filter(my_read, rm.3qual = 28)
# look at the trimmed sequences
sread(filtered)