Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • 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

        Latest Articles

        Collapse

        • seqadmin
          Essential Discoveries and Tools in Epitranscriptomics
          by seqadmin




          The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
          04-22-2024, 07:01 AM
        • seqadmin
          Current Approaches to Protein Sequencing
          by seqadmin


          Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
          04-04-2024, 04:25 PM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, 04-11-2024, 12:08 PM
        0 responses
        59 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 04-10-2024, 10:19 PM
        0 responses
        57 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 04-10-2024, 09:21 AM
        0 responses
        53 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 04-04-2024, 09:00 AM
        0 responses
        56 views
        0 likes
        Last Post seqadmin  
        Working...
        X