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  • Fastx Toolkit for Quality Stats of data from new illumina pipeline software

    Hi,

    My data is in a new format generated by the new illumina pipeline software v 1.8. So, the quality scores are in Sanger FASTQ format with ASCII offset 33.

    I used following code of Fastx tooklit to find quality stats of my data.

    root@SNP215-01:Cold_Shock_Filtered# fastx_quality_stats -Q33 -i Cold_Shock_negative_2.fq -o Cold_Shock_negative_2.fq.stats

    I received the following ERROR message:

    fastx_quality_stats: Invalid quality score value (char 'J' ord 74 quality value 41) on line 20

    So, please help me to resolve this problem.

    Thank you for your time !

    Vedbar

  • #2
    Illumina also improved the chemistry, so the PHRED score of 41 is real but higher that people are used to, 0 - 40.

    I thought fastx fixed this - which version are you using?

    Comment


    • #3
      I am using FASTX toolkit 0.0.12.

      Comment


      • #4
        Something like:

        sed s/J/I/ oldfastq.fq > newfastq.fq
        Will change all the 'J's to 'I's; that's a quick and dirty workaround. You'll be slightly lying about how awesomely high quality your letters are, because J's are a little better than I's, but it shouldn't make much difference.

        Comment


        • #5
          Originally posted by vedbar View Post
          I am using FASTX toolkit 0.0.12.
          According to http://hannonlab.cshl.edu/fastx_toolkit/ the latest release is FASTX 0.0.13, but that doesn't explicitly mention this issue. Given the release date (Feb 2010) then I doubt it will cope.

          So try v0.0.13 and if it also fails please contact the FASTX authors.

          Comment


          • #6
            Originally posted by maubp View Post
            According to http://hannonlab.cshl.edu/fastx_toolkit/ the latest release is FASTX 0.0.13, but that doesn't explicitly mention this issue. Given the release date (Feb 2010) then I doubt it will cope.

            So try v0.0.13 and if it also fails please contact the FASTX authors.
            Yes, v0.0.13 does fix this problem. See this thread/post for a more detailed explanation:

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

            Comment


            • #7
              Thank you !

              Comment

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