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  • .clocs format

    Does anyone know how to convert the .clocs files to .locs files?

    We're running a HiSeq2000 100X100 with RTA 1.12.4 RTA failed to generate .bcl files for read 2, so I am attempting to run OLB-1.9.0 bustard.py from .cifs to generate basecalls. However this version of RTA generates .clocs files and OLB needs .locs files.

    The manual states the .clocs file is a compressed version of the .locs file, but does not give any details on type of compression or how to uncompress. I have e-mailed our FAS & tech support but am told it may be a couple of days before there is an answer. I was hoping someone here has some ideas....
    Christine Brennan
    UM DNA Sequencing Core
    Ann Arbor, MI 48109

    [email protected]

  • #2
    The way I understand it, OLB 1.9 should be able to use your clocs files directly.

    "Important Changes in OLB v1.9:
    Supports formatted (_pos.txt), binary (.locs), or compressed binary (.clocs) position
    files."

    See the user guide for the following options:

    -p, --positions-directory
    -P, --positions-format

    Comment


    • #3
      Originally posted by kets View Post
      The way I understand it, OLB 1.9 should be able to use your clocs files directly.

      "Important Changes in OLB v1.9:
      Supports formatted (_pos.txt), binary (.locs), or compressed binary (.clocs) position
      files."

      See the user guide for the following options:

      -p, --positions-directory
      -P, --positions-format
      Yeah, that's what the guide says, but when I tried the -P and/or --positions-format option OLB errors with 'Failed to parse command-line options' and if you run bustard.py --help neither of those options are listed as valid. I think it only works if you're running the BclConverter
      Christine Brennan
      UM DNA Sequencing Core
      Ann Arbor, MI 48109

      [email protected]

      Comment


      • #4
        Just got the following response from Illumina:

        Currently, bustard.py is not compatible with RTA 1.12 data. You can work around the .clocs vs .locs issue by specifying "posSuffix=.clocs" when evoking 'make', i.e. the command would be

        make -j [n] posSuffix=.clocs

        Also, please be aware that this version of Bustard uses different qtables from those optimized for the latest TruSeq v3 chemistry, so your quality scores will be slightly different from those produced by RTA 1.12

        There will be a new release of OLB, version 1.9.3, coming out very shortly which will be compatible with the latest RTA and sequencing chemistry.

        It's running now....seems to be chugging along ok
        Christine Brennan
        UM DNA Sequencing Core
        Ann Arbor, MI 48109

        [email protected]

        Comment


        • #5
          Originally posted by cbrennan View Post
          Just got the following response from Illumina:

          Currently, bustard.py is not compatible with RTA 1.12 data. You can work around the .clocs vs .locs issue by specifying "posSuffix=.clocs" when evoking 'make', i.e. the command would be

          make -j [n] posSuffix=.clocs

          Also, please be aware that this version of Bustard uses different qtables from those optimized for the latest TruSeq v3 chemistry, so your quality scores will be slightly different from those produced by RTA 1.12

          There will be a new release of OLB, version 1.9.3, coming out very shortly which will be compatible with the latest RTA and sequencing chemistry.

          It's running now....seems to be chugging along ok
          Has doing this resulted in quality scores >40 (e.g. i)? Can you check in your sequence files?

          EDIT: We just heard from illumina that the new v.3 sequencing kits have had the quality range extended. The quality table for the new, v3 kits has a range from “B” to “m”.
          Last edited by GenoMax; 06-27-2011, 12:05 PM. Reason: Additional info

          Comment

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