Unconfigured Ad

Collapse
X
 
  • Time
  • Show
Clear All
new posts
  • qnc
    Member
    • Jun 2010
    • 51

    #1

    Trouble UpLoading BAM file to Galaxy

    Hi I have been trying to upload this bam file



    Which is located on this page


    All I get is:
    "http://slm22.ioo.ucl.ac.uk/~qncwork/Vanita-Ori.bam
    An error occurred setting the metadata for this dataset. You may be able to set it manually or retry auto-detection.
    error
    format: bam, database: hg19
    Info: Unable to fetch http://slm22.ioo.ucl.ac.uk/~qncwork/Vanita-Ori.bam
    [Errno socket error] [Errno 110] Connection timed out"


    I am happy to try UCSC but wanted to get a Variant's file from it to pass in Seatle Seq or something similar.

    Then ultimately wanted to map any likely changes on UCSC with a MAF file.

    But happy to look at the first stage which is getting BAM files uploaded.

    Happy to look at other BAM analysis tools as well.

    Can anyone help?
  • GenoMax
    Senior Member
    • Feb 2008
    • 7142

    #2
    The problem may be on your end. I can't access the file from the link you have provided for the bam file. Perhaps the firewall on your machine is preventing file access from outside.
    Last edited by GenoMax; 04-23-2012, 04:13 AM.

    Comment

    • qnc
      Member
      • Jun 2010
      • 51

      #3
      Looking at other threads it might be a fire wall problem.

      Is there any other site to host BAM and other large files on?

      One without download restrictions?

      Will check on the UCL Firewall status etc...

      Thanks

      Comment

      • GenoMax
        Senior Member
        • Feb 2008
        • 7142

        #4
        If this is sensitive/patient research data then you should consider setting up a local instance of galaxy rather that using the main galaxy site.

        I am sure you have seen the disclaimer on the galaxy site about protected research data but just in case ....

        Comment

        Latest Articles

        Collapse

        • SEQadmin2
          16S/ITS Profiling vs. Shotgun Metagenomics: What Changes in Your Workflow?
          by SEQadmin2




          NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification, detection...
          Today, 06:46 AM
        • SEQadmin2
          Multiomic Liquid Biopsy: What DNA/RNA Panels Reveal That DNA Alone Can’t
          by SEQadmin2



          Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?

          Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating
          ...
          10-14-2026, 09:55 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by SEQadmin2, 10-28-2026, 09:57 AM
        0 responses
        23 views
        0 reactions
        Last Post SEQadmin2  
        Started by SEQadmin2, 10-28-2026, 09:51 AM
        0 responses
        15 views
        0 reactions
        Last Post SEQadmin2  
        Started by SEQadmin2, 10-22-2026, 11:13 AM
        0 responses
        68 views
        0 reactions
        Last Post SEQadmin2  
        Started by SEQadmin2, 10-22-2026, 10:48 AM
        0 responses
        48 views
        0 reactions
        Last Post SEQadmin2  
        Working...