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  • fastx_barcode_splitter

    I used fastx_barcode_splitter.pl to demultiplex the barcodes to generate separate fastq files. However the files still retain the barcodes (at the beginning of each sequence in my case) . I want to remove those before the alignment.
    First, is there an option in fastx_barcode_splitter.pl to remove the barcodes while splitting the file? if not, I tried using:
    fastx_trimmer -f 5 -l 50 -i input.fastq -o output.fastq
    it gives the following error:
    fastx_trimmer: Invalid quality score value (char '#' ord 35 quality value -29) on line 4

    I used python script python trimmer.py -f input.fastq -s 5 -e 50 > try.fastq
    but it trims every line (not just the sequence line) leading to wrong fastq format.

    please help.
    thanks

  • #2
    Hi biofreak,
    I have exactly the same problem. Did you find any solution to the problem?

    Comment


    • #3
      You need to offset the Q scores with the -Q33 option, so instead of

      fastx_trimmer -f 5 -l 50 -i input.fastq -o output.fastq

      try

      fastx_trimmer -Q33 -f 5 -l 50 -i input.fastq -o output.fastq

      I can't believe this isn't in their documentation, but it makes everything work!

      Comment


      • #4
        thanks jme,
        but I should be more specific (and probably read the post carefully ;-) )
        My problem is:
        I want demultiplex illumina reads according to a set of 64 barcodes. I have stripped off the adapters from 3'. Subsequently I actually used sabre to demultiplex, and it worked smoothly. However, I'm unsure, whether the script retains the barcode or removes it. After looking into the fastx_barcode_splitter.pl code, I must conclude that barcode seqs are retained.
        as to your answer: my problem was not the qual settings, thanks anyway.

        Comment


        • #5
          Sorry, my fault for skimming, just saw the error!

          Comment

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