Remove a fixed number of bases of a ShortReadQ object from 3' or 5' — fixed_filter • FastqCleaner
Description: The program removes a given number of bases from the 3' or 5' regions of the sequences contained in a ShortReadQ object

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

`fixed_filter.Rd`

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

    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

## 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)#>   A DNAStringSet instance of length 6
    #>     width seq
    #> [1]    15 TGGTCCGGTGTTCTG
    #> [2]    15 ATAGGTACAGTCCAG
    #> [3]    15 GCCTCCCGCAGACGC
    #> [4]    15 CCGGAATGCCCTTTC
    #> [5]    15 AGCTCCAGCCGTTTG
    #> [6]    15 GCGGAAAGTGAACTTsread(filtered5)#>   A DNAStringSet instance of length 6
    #>     width seq
    #> [1]    15 CGGTGTTCTGGCGGA
    #> [2]    15 TACAGTCCAGTAATT
    #> [3]    15 CCGCAGACGCTGGGT
    #> [4]    15 ATGCCCTTTCTGAGC
    #> [5]    15 CAGCCGTTTGACTTC
    #> [6]    15 AAGTGAACTTAGATTsread(filtered3and5)#>   A DNAStringSet instance of length 6
    #>     width seq
    #> [1]     5 TTCTG
    #> [2]     5 TCCAG
    #> [3]     5 GACGC
    #> [4]     5 CTTTC
    #> [5]     5 GTTTG
    #> [6]     5 AACTT