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  • Struggling with quality trimming

    Hello everybody,

    this is my first try to trim Illumina (paired-end) reads on the unix command line.
    If i get it correctly, de-multiplexing was already done by the sequencing service.
    I guess this also means that the adapters are also gone already.

    What i want to do is trimming the reads by quality.
    I checked it on FastQC and want to get rid of read with a quality below 20.

    I tried trim_galore with
    trim_galore ../name1.fastq -q 20 --paired > trim_name.fastq

    which gives me:
    "No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default)
    Please provide an even number of input files for paired-end FastQ trimming! Aborting ..." <- i got the idea of this line

    But i don't really know how to find out how my data are encoded.
    The data look like this.

    @NS500339:99:H3H52AFXX:1:11101:5599:1027 2:N:0:GTGAAA
    NNNCTGGTTATAGGTACATTGAGCAACTGACTGAAATGCCTCAAAATGTTCTTTACGATGCCATTGGGATATATCAACGGTGGTATATCCAGTGATTTTTTTCTCCATTTTAGCTTCCTTAGCTCCTGAAAATCTCGANANCTCNNAAAA
    +
    ###/AEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEE<6/<EEEEEEEEAAE6EEE/EEEEEEEEEEEAAEEEEE/6EE<AEEEEAEA<EEE/EEE/AAAE#<#<A/##/<<6


    I also tried fastx toolbox with the following command
    fastq_quality_filter -q 20 -i ../name.fastq -v -o trimmed_name.fastq

    The program works,
    Minimum percentage: 0
    Input: 4564772 reads.
    Output: 4564772 reads.
    discarded 0 (0%) low-quality reads.

    but if i check it again with FastQC, there are still reads with a quality below 20.


    Maybe someone can please help me with one of the programs.

    Thanks a lot, Alex

  • #2
    Grab a copy of BBMap and then run

    Code:
    $ zcat yourfile.fastq.gz | head -20 > new.fq
    $ testformat.sh in=new.fq
    to identify the format of the encoding in your file.

    While you have a copy of BBMap handy, use bbduk.sh to do trimming.

    Code:
    $ bbduk.sh -Xmx1g in=reads.fq.gz out=clean.fq.gz qtrim=r trimq=10

    Comment


    • #3
      Thanks

      Thanks a lot, if now the following mapping step also works, this will be the solution

      Comment


      • #4
        You could stay with BBMap and use bbmap.sh to do the mapping as well.

        Comment

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