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  • zisis86
    started a topic Usage of writeFastq function from ShortRead

    Usage of writeFastq function from ShortRead

    Hi,
    I am totaly new and i have a question about the syntax of writeFastq function.
    I have this script that search for primer sequences in a file and saves good reads from fuzzy in .good.fq file and bad reads in .bad.fq file> i want to use writeFastq functions from ShortRead package to save "good" reads from fuzzy match in "*.good.fq" file and "bad" reads in *".bad.fq" file.Can you help me with the code that i have to fill in in order to do this .
    here is my code until now.

    gc()
    rm(list=ls())
    library(ShortRead)
    #library(Biostrings)

    #read bait sequences
    baitseq <- readLines("/home/users/bait_seq.txt")
    baitseq

    #choose case
    num <- 1
    exptPath <- "/home/users/INDEX1.fastq"
    exptPath

    #read data
    fq <- readFastq(dirPath=exptPath)
    sread(fq)

    #count ocurrences of bait
    pos <- grepl(baitseq[num],sread(fq))
    pos[1:25]
    # number of reads
    length(pos)
    # number of hits
    sum(pos)

    # fuzzy match - 2 substitutions
    fpos <- agrep(baitseq[num],sread(fq), max = list(sub = 2, ins=0, del=0))
    fpos[1:25]
    # number of fuzzy hits
    length(fpos)

    # writeFastq functions in ShortRead package to save "good" reads from fuzzy match in "*.good.fq" file and "bad" reads in *".bad.fq" file # ???????
    ............


    #tables
    #table <- tables(sread(fq), n=5)
    #table$top
    Last edited by zisis86; 10-20-2013, 11:32 PM.

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