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)

Arguments

input

ShortReadQ object

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?

Value

Filtered ShortReadQ object

Examples

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)
#> A DNAStringSet instance of length 6 #> width seq #> [1] 20 TGGTCCGGTGTTCTGGCGGA #> [2] 15 ATAGGTACAGTCCAG #> [3] 15 GCCTCCCGCAGACGC #> [4] 20 CCGGAATGCCCTTTCTGAGC #> [5] 20 AGCTCCAGCCGTTTGACTTC #> [6] 20 GCGGAAAGTGAACTTAGATT