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  • Extract reads from paired-end fastq based on specific adapters with bbduk

    Hello everyone, I am using bbduk.sh (from bbmap toolkit) to extract reads from paired-end fastq files based on the presence of specific adapters in the 5' of the sequence in the "_1" fastq file.

    I am using this command:

    Code:
    ./bbmap/bbduk.sh -Xmx1g in1=reads_1.fastq.gz in2=reads_2.fastq.gz outm1=matched1.fastq.gz outm2=matched2.fastq.gz literal=AAACCTGAGAAACCTA k=16 hdist=0 -rcomp=f
    The problem is that other that the correct reads, the output file contains also other reads which do not include the adapter sequence, es:

    # from reads_1.fastq.gz
    @SRR9262917.232075 232075/1
    GCATGCGAGTAGCGGTGGTTCTTATA
    +
    FFFFFFFFFFFFFFFFFFFFFFFFFF

    # from reads_2.fastq.gz
    @SRR9262917.232075 232075/2
    AAGCAGTGGTATCAACGCAGAGTACATGGGATTCCATAGCCCTGTGGTTTTTATAGATCTTGTAAACCCCAAACCTGGGAAACCTAGTGGC
    +
    FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF,FFFFFFFFF

    Does anyone know why this may be happening and how to avoid this?

    Thanks in advance.

  • #2
    You could add a "restrictleft=N" N=certain number of bases to look only in that area. Also adding "minlength=N" will exclude small reads like the first example. Also try setting k to something smaller (8) so it has better chances of matching correctly.

    I hope "-rcomp=f" is a typo. There should be no - at beginning.
    Last edited by GenoMax; 11-08-2019, 06:44 AM.

    Comment


    • #3
      Thank you! That worked

      Comment

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