Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • In search of a sign in the data: When is a HiSeq run really done?

    A maybe odd, but interesting question: Is there an easy way to see, if a HiSeq run has finished producing data, if you are not able to take a look at the HiSeq itself and its display? I mean, I would like to just look at the data it produced on our cluster and say: Hey, this run is done, because there exists a file called "run_finsihed_successfully.txt" in the run folder or something like it. Does somebody know an answer to this?

  • #2
    Yes.

    This is with a GAIIx, not a high-seq, but I have the following files appearing:
    Basecalling_Netcopy_complete.txt

    Depending of what information you want, this might also be of interest:
    ImageAnalysis_Netcopy_complete.txt

    You also have a similar file for each of the reads also.

    Comment


    • #3
      For the GAII fpepin is right, the Basecalling_Netcopy_complete_SINGLEREAD.txt or Basecalling_Netcopy_complete_READ2.txt files signal the end of the run. These are generated only when a single or paired end run is finished producing data.

      For the HiSeq, parse the RunInfo.xml file to determine the number of expected reads and then look for the corresponding Basecalling_Netcopy_complete_Read*.txt file. Here is the python code to handle both of these cases:

      https://github.com/chapmanb/bcbb/blo...ed_msg.py#L179

      Comment


      • #4
        Thanks a lot for the information (and the code!) fpepin and Brad-Chapman.

        I suppose it is a bug, that "Basecalling_Netcopy_complete.txt" is created after the first read already and not (logically) after the last one, but I can live with that.

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Strategies for Sequencing Challenging Samples
          by seqadmin


          Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
          03-22-2024, 06:39 AM
        • seqadmin
          Techniques and Challenges in Conservation Genomics
          by seqadmin



          The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

          Avian Conservation
          Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
          03-08-2024, 10:41 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, 03-27-2024, 06:37 PM
        0 responses
        13 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-27-2024, 06:07 PM
        0 responses
        12 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-22-2024, 10:03 AM
        0 responses
        53 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-21-2024, 07:32 AM
        0 responses
        69 views
        0 likes
        Last Post seqadmin  
        Working...
        X