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  • pingu
    Member
    • Jul 2015
    • 26

    Demultiplexing

    Hello,
    I have to demultiplex my fastq file, I have seen that about 200 reads are not assigned (total is 17000), there is a tool that can check barcode on 5' and 3'?
    Thank you very much
    Last edited by pingu; 09-19-2015, 02:00 AM.
  • GenoMax
    Senior Member
    • Feb 2008
    • 7142

    #2
    Are you referring to an internal barcode that is present in the read itself? Do you know what those barcodes are?

    Comment

    • pingu
      Member
      • Jul 2015
      • 26

      #3
      Thank you for your help, I know the barcodes and they are at the of the reads (last 10bp)
      For example, this read is not assigned:
      @JBMBIZC01CKLPI
      CACTGTAGAAGACTCGGCAGCATCTCCATGAGCCAGTATTGAAAATGTTGAAGATCAAAAAA
      CACTAAGTTTTTCCAAAGTTAATATCCAATGTAAAAGATAGCAAATGCATACCCACAAACTGTA
      AATGAAGATATTTGCGTTGAGGAACTTGTGACTAGCTCTTCACCCTGCAAAAATAAAAATGCA
      GCCATTAAATTGTCCATATCTAATAGTAATAATTTTGAGGTAGGGCCACCTGCATTTAGGATAG
      CCAGTGGTAAAATCGTTTGTGTTTCACATGAAACATTAAAAAAGTGAAAGACATATTTACAGA
      CAGTTTCAGTAAAGTAATTAAGGAAAACAACGAGAATAAATCAAAAATTTGCCAAACGAAAA
      TTATGGCAGGTTGTTTGGAGAACAGTGACGATCGCCTACAGTGCT

      The barcodes of the reads is: AGCACTGTAG and it is a complementary reverse: CTACAGTGCT,
      I have MID at the start of the reads (5') e at the end (3'), the barcode splitter tool checks MID at 5' and I have allowed 2 mismatches.
      Last edited by pingu; 09-19-2015, 01:28 PM.

      Comment

      • sklages
        Senior Member
        • May 2008
        • 628

        #4
        Looks like 454 data. If you have the original SFF file you could use Roche's sfffile tool to demultiplex your data. It recognizes 5' and 3' barcodes/MIDs.

        Comment

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