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  1. IGB
  2. IGBF-2696

Add blacklist regions to IGB quickload for mouse, human, fruit fly

    Details

    • Story Points:
      1.5
    • Sprint:
      Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5, Spring 6 2021 May 31 - June 11, Summer 1 2021 Jun 14 - Jun 25, Summer 2 2021 Jun 28 - Jul 9, Summer 3 2021 Jul 12 - Jul 23, Summer 4 2021 Aug 2 - Aug 13, Fall 1 2021 Aug 16 - Aug 27, Fall 2 2021 Aug 30 - Sep10, Fall 3 2021 Sep 13 - Sep 24

      Description

      "blacklist" genes are genes or regions in a genome that give bizarre results in sequence-based assays.

      Let's include these in IGB.

      This github repo directory contains bed files with blacklisted regions:

      References:

      Visualizations:

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            Hide
            nfreese Nowlan Freese added a comment -

            All of the blacklist files have been pushed to the SVN repository, with the exception of dm6.

            I have created IGBF-2955 to address pushing the changes to the SciDas and Quickload servers.

            Show
            nfreese Nowlan Freese added a comment - All of the blacklist files have been pushed to the SVN repository, with the exception of dm6. I have created IGBF-2955 to address pushing the changes to the SciDas and Quickload servers.
            Hide
            ann.loraine Ann Loraine added a comment -

            Please don't test until sites are updated and deployed. (Sorry - I moved this forward to "ready for testing" prematurely.)

            Show
            ann.loraine Ann Loraine added a comment - Please don't test until sites are updated and deployed. (Sorry - I moved this forward to "ready for testing" prematurely.)
            Hide
            ann.loraine Ann Loraine added a comment -

            Now it is ready for testing.
            attn: Nowlan Freese

            Show
            ann.loraine Ann Loraine added a comment - Now it is ready for testing. attn: Nowlan Freese
            Hide
            nfreese Nowlan Freese added a comment -

            Discrepancy - While testing I noticed that in the C_elegans_oct_2010 (ce10) genome the blacklist region was outside of the range of some of the chromosomes (i.e. the blacklist regions were greater than the max chromosome size). The genome length in IGB (C_elegans_oct_2010) is correct when compared to UCSC. I also re-downloaded the ce10 blacklist file. It appears that the locations of some of the blacklist regions are incorrect or mis-annotated, indicating an issue with the pipeline that the blacklist authors used.

            Show
            nfreese Nowlan Freese added a comment - Discrepancy - While testing I noticed that in the C_elegans_oct_2010 (ce10) genome the blacklist region was outside of the range of some of the chromosomes (i.e. the blacklist regions were greater than the max chromosome size). The genome length in IGB (C_elegans_oct_2010) is correct when compared to UCSC. I also re-downloaded the ce10 blacklist file. It appears that the locations of some of the blacklist regions are incorrect or mis-annotated, indicating an issue with the pipeline that the blacklist authors used.
            Hide
            nfreese Nowlan Freese added a comment -

            Testing complete, no issues.

            Closing ticket.

            Show
            nfreese Nowlan Freese added a comment - Testing complete, no issues. Closing ticket.

              People

              • Assignee:
                nfreese Nowlan Freese
                Reporter:
                ann.loraine Ann Loraine
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                Dates

                • Created:
                  Updated:
                  Resolved: