Filter sequences with low quality in 3' tails — trim3q_filter • FastqCleaner
Description: The program removes from the 3' tails of the sequences a set of nucleotides showing a quality &lt; a threshold value in a ShortReadQ object

# Filter sequences with low quality in 3' tails

`trim3q_filter.Rd`

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