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  • phred 33 or 64

    Hello,

    I am trying to use Trimmomatic to trim adaptor, and really confusing about my file is phred +33 or phred +64?


    @J00160:122:HT2VJBBXX:8:1101:23348:1261 1:N:0:ATTACTCG+AGGCNATA
    GNCTTAAATCGTGTTCCAAACCAAAATGATACAATCATGTCTCTGTTCAGCTGGGCCCANACATAAAGTACTGACNTGNTCAGNGGNANCNTCAGCAACTG
    +
    A#AFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJFJJJFJJFJJJJJJ#JJJJJJFJJJJJJJJ#AA#7AJJ#FF#J#F#JJJAJJJJJJ
    @J00160:122:HT2VJBBXX:8:1101:23449:1261 1:N:0:ATTACTCG+AGGCNATA
    GNCTGTTTCAGGCAGGGCTTACACTCTTCCCAGAGGGCCATCATGGTCTCATTGCACACNCCTGGGAGCTCCTTCNGCNTTGTNTCNGNTNCCCTGGTCTC
    +
    A#AFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJ#JJJJJJJJJJJJJJJ#AJ#FJJJ#JJ#J#J#JJJJJJJJJJ
    @J00160:122:HT2VJBBXX:8:1101:23896:1261 1:N:0:ATTACTCG+AGGCTATA
    CCAATCTTCTCCACACAGCCCTCCTTATGGATCGCCTTCTCGTTGAAATTAATCCCACANCCCACAGTAACATTAATGNAGCANGANTNGNGGACTCGGTT
    +
    AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ#JJJJJJJJJJJJJJJJJJ#JJJJ#JJ#J#J#JJJJFJJJFF




    Thanks in advance for great help!


    Yue Li

  • #2
    All new data should be phred+33. If you have data that is 5+ yr old then you have to worry about it being phred+33.

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    • #3
      Thank you so much GenoMax!

      Comment


      • #4
        It is actually easy to spot (see the table here): in Phred + 33, capital letters are at the top end of the quality range (Phred score plus 33 gives an ASCII code for a capital letter when Phred is 32 to 42), while a capital letter would be an abysmal score in Phred +64. And in your case, you have "#" which is only valid for Phred +33 (ASCII code 35).

        Comment


        • #5
          r.rosati,

          Thanks for helping!

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