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  • GApipeline version / paired-end discovery

    Hi,
    I've got 2 doubts:
    1) how can I see which version of GApipeline was used to analyze my data? Is there a particular file to search in?
    2) how can I distinguished if it has been performed a single or paired-end sequencing procedure from my FASTQ file?
    Thank you a lot

  • #2
    The name of the firecrest folder should tell you for ex:
    C1-40_Firecrest1.4.0_22-10-2009_seqlab
    This was analyzed with pipeline v1.4

    For more detail, inside your Firecrest folder you should find support.txt that contains the exact command line used to kick off the pipeline.

    Your Firecrest makefile will also contain the --start_next_read parameter. It gets this info from the run.params file at the top level of the run folder. If necessary it can be overridden by deleting the run.parameters file and feeding the argument directly from the command line.
    Christine Brennan
    UM DNA Sequencing Core
    Ann Arbor, MI 48109

    [email protected]

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    • #3
      Originally posted by username View Post
      Hi,
      how can I distinguished if it has been performed a single or paired-end sequencing procedure from my FASTQ file?
      If you've got the original FastQ file then you can tell from the filename itself. Single end reads will have a name like:

      s_1_sequence.txt

      whereas paired end reads will have an extra number denoting the read:

      s_1_1_sequence.txt

      From within the file I'm not sure you can tell the difference between a single end run and the first end of a paired end run since they will both have IDs which look like:

      +HWUSI-EAS493:1:1:1:1079#0/1

      ..where the /1 denotes the first read. The second read of a paired end run will have a corresponding

      +HWUSI-EAS493:1:1:1:1079#0/2

      ..read in the other ends FastQ file, but the first end will still look like a single end file.

      Comment


      • #4
        Originally posted by simonandrews View Post
        If you've got the original FastQ file then you can tell from the filename itself. Single end reads will have a name like:

        s_1_sequence.txt

        whereas paired end reads will have an extra number denoting the read:

        s_1_1_sequence.txt

        From within the file I'm not sure you can tell the difference between a single end run and the first end of a paired end run since they will both have IDs which look like:

        +HWUSI-EAS493:1:1:1:1079#0/1

        ..where the /1 denotes the first read. The second read of a paired end run will have a corresponding

        +HWUSI-EAS493:1:1:1:1079#0/2

        ..read in the other ends FastQ file, but the first end will still look like a single end file.
        Thank you a lot for the answer, it was really very useful! Bye

        Comment


        • #5
          Originally posted by cbrennan View Post
          The name of the firecrest folder should tell you for ex:
          C1-40_Firecrest1.4.0_22-10-2009_seqlab
          This was analyzed with pipeline v1.4

          For more detail, inside your Firecrest folder you should find support.txt that contains the exact command line used to kick off the pipeline.

          Your Firecrest makefile will also contain the --start_next_read parameter. It gets this info from the run.params file at the top level of the run folder. If necessary it can be overridden by deleting the run.parameters file and feeding the argument directly from the command line.
          Thank you! So, the GApipeline version used was the 1.9.5, but the problem is that this doesn't match with the ASCII characters encoding the quality values in my file, because they are from 59 to 126... mmh... should it be that in the 1.9.5 version Solexa software's developers returned back to the old coding (like until version 1.3)?

          Comment

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