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  • 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?

  • #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


    • #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


      • #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

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