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  • Zipped BCL to FastQ

    Hi Friends,

    When I used CASAVA 1.8.2 to convert BCL to FastQ, it showd and error that *.bcl file not found. When I go to folder to check for the file i found *.bcl.gz file was present. In this way the conversion has failed.

    Dear Friends, Is there any new command how to convert those zipped BCL file to FastQ format ?

    Thanks.
    Amit

  • #2
    Amit: It appears that you have data generated by a new version of HiSeq control software where the provider selected the option to zip the bcl files.

    You will need to get bcl2fastq (v.1.8.3) software to handle the zipped files. You can download it here: http://support.illumina.com/download...tware_183.ilmn

    Your data is likely to also have the Q-score binning applied as described in this white paper. http://support.illumina.com/download...footprint.ilmn.
    Last edited by GenoMax; 03-11-2013, 04:04 AM.

    Comment


    • #3
      Dear GenoMax,

      Thanks a lot for the reply, YEs our HiSeq got upgraded to 2500 from 2000 and hence the option of Zipped BCL file have been selected.

      I have followed you instructions and the job has been completed succefully

      Gr8 !

      Thanks again.

      Best
      Amit Chaurasia

      Comment


      • #4
        Just an update: the new version of BCL2FASTQ is out (v1.8.4):
        This download contains the software, release notes, and user guide for the 1.8.4. version of the Bcl2FastQ conversion software. The Bcl2FastQ conversion software is a tool to handle bcl conversion and demultiplexing. Version 1.8.4 has added ability to mask multiple adapter sequences per read, has standard Illumina adapter sequences included in the bcl2fastq installation, and the stringency of the adapter masking feature is now configurable.


        It has improved the adaptor cleaning and the trimming is different.

        Comment

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