Uploaded image for project: 'IGB'
  1. IGB
  2. IGBF-2952

Add UCSC dm6 fruit fly genome and annotation to IGB

    Details

    • Story Points:
      1.5
    • Sprint:
      Fall 3 2021 Sep 13 - Sep 24, Fall 6 2021 Oct 25 - Nov 5, Fall 7 2021 Nov 8 - Nov 24, Fall 8 2021 Nov 29 - Dec 10

      Description

      Situation: A discrepancy was identified in the current released version of the dm6 genome in IGB and the genome available through UCSC. This may confuse users who attempt to load data using UCSC DAS.

      Task: Add the UCSC dm6 genome and annotation to IGB.

        Attachments

        1. screenshot-1.png
          screenshot-1.png
          151 kB
        2. screenshot-2.png
          screenshot-2.png
          144 kB
        3. screenshot-3.png
          screenshot-3.png
          131 kB
        4. screenshot-4.png
          screenshot-4.png
          106 kB

          Issue Links

            Activity

            Hide
            ann.loraine Ann Loraine added a comment -

            Deployed to:

            and ready for testing.

            attn:

            Nowlan Freese
            Omkar Marne

            Show
            ann.loraine Ann Loraine added a comment - Deployed to: Quickload hosted at UNC Charlotte: http://igbquickload.org/quickload/ Quickload hosted at RENCI: http://lorainelab-quickload.scidas.org/quickload Quickload hosted on Amazon EC2: http://quickload.bioviz.org/quickload/ and ready for testing. attn: Nowlan Freese Omkar Marne
            Hide
            nfreese Nowlan Freese added a comment -

            To test:
            In IGB,

            1. Disable all Data Sources
            2. Add one of the above data sources
            3. Select the Drosophila melanogaster Species and the D_melanogaster_Aug_2014 Genome Version.
            4. The RefGene track should appear and should automatically load data.
            5. Navigate to: chrX:6,206,883-6,206,926
            6. Click Load Sequence.
            7. Residues (ATCG) should load.
            8. Check that there are no errors in the log.
            9. Select the ENCODE blacklist under Available Data.
            10. Navigate to: chr2R:737,475-885,425
            11. Click Load Data
            12. Data should load in view (should appear as a black bar titled Low Mappability).
            13. Check that there are no errors in the log.
            14. Enable the UCSC DAS data provider as a Data Source.
            15. The UCSC (DAS) folder should appear under Available Data in the Data Access tab.
            16. Select the ensGene.
            17. Click Load Data.
            18. Check that there are no errors in the log.

            Repeat the above steps for all three Quickload hosts.

            Show
            nfreese Nowlan Freese added a comment - To test: In IGB, Disable all Data Sources Add one of the above data sources Select the Drosophila melanogaster Species and the D_melanogaster_Aug_2014 Genome Version. The RefGene track should appear and should automatically load data. Navigate to: chrX:6,206,883-6,206,926 Click Load Sequence . Residues (ATCG) should load. Check that there are no errors in the log. Select the ENCODE blacklist under Available Data. Navigate to: chr2R:737,475-885,425 Click Load Data Data should load in view (should appear as a black bar titled Low Mappability). Check that there are no errors in the log. Enable the UCSC DAS data provider as a Data Source. The UCSC (DAS) folder should appear under Available Data in the Data Access tab. Select the ensGene. Click Load Data. Check that there are no errors in the log. Repeat the above steps for all three Quickload hosts.
            Hide
            omarne Omkar Marne (Inactive) added a comment - - edited

            I added Quickload hosted on Amazon EC2 http://quickload.bioviz.org/quickload/ data source and followed above steps. All the steps performed as expected.

            I couldn't load below data sources because they were already present in the data sources tab.

            Please refer screenshot 4.

            Show
            omarne Omkar Marne (Inactive) added a comment - - edited I added Quickload hosted on Amazon EC2 http://quickload.bioviz.org/quickload/ data source and followed above steps. All the steps performed as expected. I couldn't load below data sources because they were already present in the data sources tab. Quickload hosted at UNC Charlotte: http://igbquickload.org/quickload/ Quickload hosted at RENCI: http://lorainelab-quickload.scidas.org/quickload Please refer screenshot 4.
            Hide
            ann.loraine Ann Loraine added a comment -

            Omkar Marne - if you disable all data sources (step 1) you should be able to add all three, even though they are already in IGB. Please try again.

            Show
            ann.loraine Ann Loraine added a comment - Omkar Marne - if you disable all data sources (step 1) you should be able to add all three, even though they are already in IGB. Please try again.
            Hide
            omarne Omkar Marne (Inactive) added a comment -

            I disable all the data sources and added the above three. I am getting the expected output.

            Closing the ticket.

            Show
            omarne Omkar Marne (Inactive) added a comment - I disable all the data sources and added the above three. I am getting the expected output. Closing the ticket.

              People

              • Assignee:
                nfreese Nowlan Freese
                Reporter:
                nfreese Nowlan Freese
              • Votes:
                0 Vote for this issue
                Watchers:
                3 Start watching this issue

                Dates

                • Created:
                  Updated:
                  Resolved: