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  • PHSchi
    Member
    • Jun 2010
    • 12

    #1

    qseq.txt to fq reloaded

    Hi! I am trying to convert Illumina qseq.txt looking like this
    HWUSI-EAS488 1 1 54 0 973 0 1 .......................................................................................................... BBBBBBB
    BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
    HWUSI-EAS488 1 1 54 0 1367 0 1 ......

    to fq using the qseq2fastq.pl posted here by Xi Wang.
    However, the resulting fastq (or fq) files come out like this
    @HWUSI-EAS488:1:1:0:1398#0/2
    ..........................................................................................................
    +
    BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
    @HWUSI-EAS488:1:1:0:167#0/2
    .........................................................................................................

    ,which for me seems to hold no sequence information, as I expected something like this:
    @1:2:12:1486
    TATAACATGGGANATGTTATAGTATNNNNNNNNTTAAAACATTNNANNNGNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
    +1:2:12:1486
    aaaaa`a_aa[ZDZ`a^`_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
    @1:2:12:2015
    CCAACCTGCTTTNGAGGCATAGACANNNNNNNNCTCATGTACANNTNNNANNCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
    +1:2:12:2015
    `bba_aababaZDW^`abbbbbbbYDDDDDDDD\aaabbBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
    .
    Or am I actually mixing up different formats?
    Thanks!
    P
  • PHSchi
    Member
    • Jun 2010
    • 12

    #2
    Ah, okay, should do more wikipedia before posting...

    Comment

    • Daniel Su
      Junior Member
      • Jun 2010
      • 2

      #3
      Yes, your descriptions of the two format are right. However, the qseq-format sequence you posted does not have signals.(that's .................................................. .................................................. ......)

      You may try other sequences (in your qseq.txt).

      Comment

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