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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
        • Epic Link:
        • 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:

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-2955 Update SciDas and IGB Quickload for blacklist

              • Major - Major loss of function.
              • Closed

              Updated Genome - After a genome has been updated and committed to SVN IGBF-2952 Add UCSC dm6 fruit fly genome and annotation to IGB

              • Major - Major loss of function.
              • Closed

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-1217 add Genome in a Bottle data sets to IGB Quickload

              • Major - Major loss of function.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                ann.loraine Ann Loraine created issue -
                ann.loraine Ann Loraine made changes -
                Field Original Value New Value
                Epic Link IGBF-1765 [ 17855 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-1217 [ IGBF-1217 ]
                ann.loraine Ann Loraine made changes -
                Summary Add blacklist genes to human genome in IGB Add blacklist genes to IGB
                ann.loraine Ann Loraine made changes -
                Description "blacklist" genes are genes or regions in the human genome that give bizarre results in sequence-based assays.

                Let's include these in IGB.

                See:

                https://www.nature.com/articles/s41598-019-45839-z

                and
                 https://www.biostars.org/p/171354/#:~:text=Here%2C%20we%20define%20the%20ENCODE,of%20cell%20line%20or%20experiment.

                For a visualization, also see:

                * https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3477-y
                * https://tarpan.shinyapps.io/tarpan/ (click "blacklist" option)                 		"blacklist" genes are genes or regions in a genome that give bizarre results in sequence-based assays.

                Let's include these in IGB.

                References:

                * https://www.nature.com/articles/s41598-019-45839-z
                *

                Visualizations:

                * Tarpan: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3477-y
                * Tarpan: https://tarpan.shinyapps.io/tarpan/ (click "blacklist" option)
                ann.loraine Ann Loraine made changes -
                Sprint Fall 7 Dec 14 - Dec 23 [ 110 ] Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8 [ 110, 111 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Summary Add blacklist genes to IGB Add blacklist genes to IGB quickload for mouse, human, fruit fly
                ann.loraine Ann Loraine made changes -
                Summary Add blacklist genes to IGB quickload for mouse, human, fruit fly Add blacklist regions to IGB quickload for mouse, human, fruit fly
                ann.loraine Ann Loraine made changes -
                Description "blacklist" genes are genes or regions in a genome that give bizarre results in sequence-based assays.

                Let's include these in IGB.

                References:

                * https://www.nature.com/articles/s41598-019-45839-z
                *

                Visualizations:

                * Tarpan: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3477-y
                * Tarpan: https://tarpan.shinyapps.io/tarpan/ (click "blacklist" option)                 		"blacklist" genes are genes or regions in a genome that give bizarre results in sequence-based assays.

                Let's include these in IGB.

                References:

                * https://www.nature.com/articles/s41598-019-45839-z

                Visualizations:

                * Tarpan: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3477-y
                * Tarpan: https://tarpan.shinyapps.io/tarpan/ (click "blacklist" option)
                ann.loraine Ann Loraine made changes -
                Comment [ This github repo directory contains bed files with blacklisted regions:

                * https://github.com/Boyle-Lab/Blacklist/tree/master/lists ]
                ann.loraine Ann Loraine made changes -
                Description "blacklist" genes are genes or regions in a genome that give bizarre results in sequence-based assays.

                Let's include these in IGB.

                References:

                * https://www.nature.com/articles/s41598-019-45839-z

                Visualizations:

                * Tarpan: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3477-y
                * Tarpan: https://tarpan.shinyapps.io/tarpan/ (click "blacklist" option)                 		"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:

                * https://github.com/Boyle-Lab/Blacklist/tree/master/lists

                References:

                * https://www.nature.com/articles/s41598-019-45839-z

                Visualizations:

                * Tarpan: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3477-y
                * Tarpan: https://tarpan.shinyapps.io/tarpan/ (click "blacklist" option)
                ann.loraine Ann Loraine made changes -
                Sprint Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8 [ 110, 111 ] Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22 [ 110, 111, 112 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22 [ 110, 111, 112 ] Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5 [ 110, 111, 112, 113 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                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 [ 110, 111, 112, 113 ] 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 [ 110, 111, 112, 113, 114 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                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 [ 110, 111, 112, 113, 114 ] 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 [ 110, 111, 112, 113, 114, 115 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Assignee Philip Badzuh [ pbadzuh ]
                ann.loraine Ann Loraine made changes -
                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 [ 110, 111, 112, 113, 114, 115 ] 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, Winter 6 Mar 8 - Mar 19 [ 110, 111, 112, 113, 114, 115, 116 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Assignee Philip Badzuh [ pbadzuh ]
                ann.loraine Ann Loraine made changes -
                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, Winter 6 Mar 8 - Mar 19 [ 110, 111, 112, 113, 114, 115, 116 ] 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 [ 110, 111, 112, 113, 114, 115 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
                nfreese Nowlan Freese made changes -
                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 [ 110, 111, 112, 113, 114, 115 ] 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 [ 110, 111, 112, 113, 114, 115, 122 ]
                nfreese Nowlan Freese made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                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 [ 110, 111, 112, 113, 114, 115, 122 ] 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 [ 110, 111, 112, 113, 114, 115, 122, 123 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
                ann.loraine Ann Loraine made changes -
                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 [ 110, 111, 112, 113, 114, 115, 122, 123 ] 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 [ 110, 111, 112, 113, 114, 115, 122, 123, 124 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                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 [ 110, 111, 112, 113, 114, 115, 122, 123, 124 ] 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 [ 110, 111, 112, 113, 114, 115, 122, 123, 124, 125 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                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 [ 110, 111, 112, 113, 114, 115, 122, 123, 124, 125 ] 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 [ 110, 111, 112, 113, 114, 115, 122, 123, 124, 125, 126 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                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 [ 110, 111, 112, 113, 114, 115, 122, 123, 124, 125, 126 ] 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 [ 110, 111, 112, 113, 114, 115, 122, 123, 124, 125, 126, 127 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                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 [ 110, 111, 112, 113, 114, 115, 122, 123, 124, 125, 126, 127 ] 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 - Aug 10 [ 110, 111, 112, 113, 114, 115, 122, 123, 124, 125, 126, 127, 128 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                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 [ 110, 111, 112, 113, 114, 115, 122, 123, 124, 125, 126, 127, 128 ] 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 2021Sep 13 - Sep 24 [ 110, 111, 112, 113, 114, 115, 122, 123, 124, 125, 126, 127, 128, 129 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
                nfreese Nowlan Freese made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                nfreese Nowlan Freese made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                nfreese Nowlan Freese made changes -
                Attachment blacklist_v2.zip [ 16782 ]
                nfreese Nowlan Freese made changes -
                Attachment blacklist_v2.zip [ 16782 ]
                nfreese Nowlan Freese made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ] Ann Loraine [ aloraine ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-2952 [ IGBF-2952 ]
                nfreese Nowlan Freese made changes -
                Assignee Ann Loraine [ aloraine ] Nowlan Freese [ nfreese ]
                nfreese Nowlan Freese made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                nfreese Nowlan Freese made changes -
                Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
                nfreese Nowlan Freese made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-2955 [ IGBF-2955 ]
                nfreese Nowlan Freese made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                ann.loraine Ann Loraine made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                nfreese Nowlan Freese made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
                nfreese Nowlan Freese made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                nfreese Nowlan Freese made changes -
                Attachment 2696.txt [ 16784 ]
                nfreese Nowlan Freese made changes -
                Fix Version/s 9.1.10 Major Release [ 10700 ]
                nfreese Nowlan Freese made changes -
                Issue Type Task [ 3 ] New Feature [ 2 ]
                nfreese Nowlan Freese made changes -
                Issue Type New Feature [ 2 ] Updated Genome [ 11 ]

                  People

                  • Assignee:
                    nfreese Nowlan Freese
                    Reporter:
                    ann.loraine Ann Loraine
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    2 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: