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  • different results from fastQC and fastx toolkits

    Hi,

    I am using fastQC to check the quality of my miRNA seq data after adaptor trimming. Then I used fastq_quality_boxplot_graph.sh from fastx toolkits to see if the results are the same as fastQC. Surprisingly, it seems that with fastq_quality_boxplot_graph.sh, the quality scores are lower (some below 30) whereas they are all above 30 using fastQC.

    Could anybody tell me why there is so big difference?

    There is another thread:
    Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc


    But in my case, I believe that all the reads have been read by fastQC or fastq_quality_boxplot_graph.sh, which can be known from their statistics.

    There is indeed a very small percentage of reads which contain N. Could that be the problem? I am looking for some tools to get rid of the reads with N.

    Attached are the results from fastQC and fastq_quality_boxplot_graph.sh. Thanks.
    Click image for larger version

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Name:	fastx_tool.png
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ID:	308158

  • #2
    Fastqc is smart and detected that your quality encoding. Fastq_quality_boxplot is not smart and didn't detect your encoding. As such, the later is plotting your scores on the solexa quality scale...hence values below zero.

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    • #3
      try http://edwards.sdsu.edu/cgi-bin/prinseq/prinseq.cgi

      Comment


      • #4
        Originally posted by JackieBadger View Post
        Fastqc is smart and detected that your quality encoding. Fastq_quality_boxplot is not smart and didn't detect your encoding. As such, the later is plotting your scores on the solexa quality scale...hence values below zero.

        http://en.wikipedia.org/wiki/FASTQ_format
        Hi,
        Thanks for your reply. The input of Fastq_quality_boxplot is the text file produced by fastx_quality_stats. I have specified -Q33 in fastx_quality_stats to get the test file. In this way, the encoding should be detected. And do you mean that results from fastQC are more reliable?

        Comment


        • #5
          Take a look at what the program actually does.

          "FASTQ Quality Chart

          $ fastq_quality_boxplot_graph.sh -h
          Solexa-Quality BoxPlot plotter
          Generates a solexa quality score box-plot graph "

          So unless you have Solexa encoding, its no use to you.

          FastqToolkit is glitchy and kind of out dated..... people have re-written many of the functions to perform better
          Last edited by JackieBadger; 06-18-2013, 10:49 AM.

          Comment


          • #6
            Originally posted by JackieBadger View Post
            Take a look at what the program actually does.

            "FASTQ Quality Chart

            $ fastq_quality_boxplot_graph.sh -h
            Solexa-Quality BoxPlot plotter
            Generates a solexa quality score box-plot graph "

            So unless you have Solexa encoding, its no use to you.

            FastqToolkit is glitchy and kind of out dated..... people have re-written many of the functions to perform better
            Ok, thanks.

            Comment

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