Unconfigured Ad

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts
  • Giles
    Member
    • Feb 2010
    • 39

    Galaxy and gz files

    I have all of a sudden become completely unable to upload any .gz files to galaxy. This is causing my work to come to a screeching halt, so if there is anyone out there who can help me understand why, please, I'm despearte.
    Specifically, the files are the tagalign.gz files from both the broad institute and UW histone tracks from the encode project. I have been able to upload these files in the past, but for some reason they just remain "blue" forever.
    please..I'm uber frustrated right now.
  • maubp
    Peter (Biopython etc)
    • Jul 2009
    • 1544

    #2
    Are you uploading from your machine, or do you give Galaxy the URL of the file hosted by the Broad Institute or UW?

    Comment

    • Giles
      Member
      • Feb 2010
      • 39

      #3
      I am first downloading the data to my machine from UCSC and then re-uploading it. The catch is that these datasets have been successfully uploaded, by me, before. But for some reason they won't go past the 'blue' button stage. It really bothers me that it seems stochastic, and I'm certain that there is something that I am missing.

      Comment

      • maubp
        Peter (Biopython etc)
        • Jul 2009
        • 1544

        #4
        It could be something changed locally on your network. While waiting for the Galaxy team to comment, can you try the direct upload from Broad Institute / UW straight into Galaxy?

        Comment

        • Giles
          Member
          • Feb 2010
          • 39

          #5
          I can't find a URL from the Broad Institute. I think it may just be a size issue. I found a smaller sample, that is in the exact same format, and it uploaded almost immediately. I suppose I'll just have to be patient.

          If you are familiar with a deposit of URLs from the Broad Institute, I'd love it if you could share it with me. I found one, but they only have a subset of the data that is available via UCSC. I'm particularly interested in K562 datasets.

          Thanks.

          Comment

          Latest Articles

          Collapse

          • SEQadmin2
            From Collection to Sequencing: Why Sample Preparation and Preservation Define Sequencing Data
            by SEQadmin2


            Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.


            The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
            ...
            06-02-2026, 10:05 AM
          • SEQadmin2
            Single-Cell Sequencing at an Inflection Point: Early Impacts of New Platforms and Emerging Trends
            by SEQadmin2


            With the launch of new single-cell sequencing platforms in 2026, the field stands at an exciting inflection point. This article surveys the most impactful advances in the field and discusses how they’re reshaping research in cancer, immunology, and beyond.


            Introduction

            Single-cell sequencing technologies have undergone remarkable advances over the past decade, transitioning from low-throughput experimental approaches to highly scalable platforms capable of...
            05-22-2026, 06:42 AM
          • SEQadmin2
            Environmental Genomics in the Age of NGS: From Microbes to Conservation Strategies
            by SEQadmin2

            Studying ecosystems means dealing with complex, multi-species communities that are hard to observe at scale. This complexity, however, hides many important questions to be answered, from how biogeochemical cycles work and how climate change can affect species distribution to how conservation strategies can work best.


            Genomics, particularly since the expansion of NGS, has transformed ecosystem ecology. By sequencing environmental DNA, we can now assess biodiversity without direct...
            05-06-2026, 09:04 AM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by SEQadmin2, Yesterday, 08:59 AM
          0 responses
          12 views
          0 reactions
          Last Post SEQadmin2  
          Started by SEQadmin2, 06-02-2026, 12:03 PM
          0 responses
          21 views
          0 reactions
          Last Post SEQadmin2  
          Started by SEQadmin2, 06-02-2026, 11:40 AM
          0 responses
          18 views
          0 reactions
          Last Post SEQadmin2  
          Started by SEQadmin2, 05-28-2026, 11:40 AM
          0 responses
          31 views
          0 reactions
          Last Post SEQadmin2  
          Working...