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  1. IGB
  2. IGBF-1498

Add C.albicans WO-1 Dec 2013 Assembly

        Details

        • Type: Updated Genome
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None
        • Story Points:
          1
        • Epic Link:
        • Sprint:
          Spring 2019 Sprint 2, Spring 2019 Sprint 3, Spring 2019 Sprint 4, Spring 2019 Sprint 5, Fall 2019 Sprint 2, Fall 2019 Sprint 3

          Attachments

            Activity

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            Jill Jill Jenkins (Inactive) created issue -
            Jill Jill Jenkins (Inactive) made changes -
            Field Original Value New Value
            Status Open [ 1 ] In Progress [ 3 ]
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            Jill Jill Jenkins (Inactive) added a comment -

            .2bit has been added.
            Features file is added and needs testing.
            HEADER.md for non-UCSC

            Show
            Jill Jill Jenkins (Inactive) added a comment - .2bit has been added. Features file is added and needs testing. HEADER.md for non-UCSC
            Jill Jill Jenkins (Inactive) made changes -
            Sprint Winter 2018 Sprint 3 [ 58 ]
            Jill Jill Jenkins (Inactive) made changes -
            Rank Ranked higher
            Jill Jill Jenkins (Inactive) made changes -
            Status In Progress [ 3 ] In Progress [ 3 ]
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            Jill Jill Jenkins (Inactive) added a comment -

            Features look good in IGB.
            Added README.md

            Show
            Jill Jill Jenkins (Inactive) added a comment - Features look good in IGB. Added README.md
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            Jill Jill Jenkins (Inactive) added a comment -

            Removed README.md should be HEADER.md

            Show
            Jill Jill Jenkins (Inactive) added a comment - Removed README.md should be HEADER.md
            ann.loraine Ann Loraine made changes -
            Sprint Spring 2019 Sprint 2 [ 60 ]
            ann.loraine Ann Loraine made changes -
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            ann.loraine Ann Loraine made changes -
            Sprint Spring 2019 Sprint 2 [ 60 ]
            ann.loraine Ann Loraine made changes -
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            Jill Jill Jenkins (Inactive) added a comment -

            Field14 not detected in IGB. Working solution.

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            Jill Jill Jenkins (Inactive) added a comment - Field14 not detected in IGB. Working solution.
            Jill Jill Jenkins (Inactive) made changes -
            Sprint Spring 2019 Sprint 2 [ 60 ]
            Jill Jill Jenkins (Inactive) made changes -
            Rank Ranked lower
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            Jill Jill Jenkins (Inactive) added a comment -

            Sorting is causing an issue with IGB detecting field14 in the BED file.

            Show
            Jill Jill Jenkins (Inactive) added a comment - Sorting is causing an issue with IGB detecting field14 in the BED file.
            Jill Jill Jenkins (Inactive) made changes -
            Attachment Standard Procedure Output.pdf [ 14272 ]
            Jill Jill Jenkins (Inactive) made changes -
            Attachment Standard Procedure Output.pdf [ 14272 ]
            Jill Jill Jenkins (Inactive) made changes -
            Attachment Standard Procedure Output.pdf [ 14273 ]
            Jill Jill Jenkins (Inactive) made changes -
            Attachment IGB view Std Procedure Output.pdf [ 14274 ]
            Jill Jill Jenkins (Inactive) made changes -
            Attachment Sublime view Std Proced Output.pdf [ 14275 ]
            Jill Jill Jenkins (Inactive) made changes -
            Attachment Reformatted file.pdf [ 14276 ]
            Jill Jill Jenkins (Inactive) made changes -
            Attachment Sublime Reformatted file.pdf [ 14277 ]
            Jill Jill Jenkins (Inactive) made changes -
            Attachment IGB view Reformatted file.pdf [ 14278 ]
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            Jill Jill Jenkins (Inactive) added a comment - - edited

            FILES attached —
            Sorting the bed file by protocol (-k1,1 -k2,2n) is causing a formatting error between lines 1-14 and 15 - 6160. This is preventing IGB from displaying field 14 (See IGB view Std Out). Two tab spaces are required from lines 15 - 6160 to resolve the issue. I need to add an additional tab space after field1 of each line from 15-6160.

            If the extra tab space is added - IGB functions as expected. See IGB view Reformatted.

            Show
            Jill Jill Jenkins (Inactive) added a comment - - edited FILES attached — Sorting the bed file by protocol (-k1,1 -k2,2n) is causing a formatting error between lines 1-14 and 15 - 6160. This is preventing IGB from displaying field 14 (See IGB view Std Out). Two tab spaces are required from lines 15 - 6160 to resolve the issue. I need to add an additional tab space after field1 of each line from 15-6160. If the extra tab space is added - IGB functions as expected. See IGB view Reformatted.
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            Jill Jill Jenkins (Inactive) added a comment -

            Sublime shows single tab space between field1&2 (lines15-end) but IGB is interpreting the tab as just a space. Replacing the whitespace between fields1&2 with space OR tab aligns the fields the same. There might be something with how IGB is interpreting that space therefore how it's displaying field14.

            If two tab spaces between fields 1&2 are used to align lines 15-6160 to 1-14, IGB correctly displays description.

            Show
            Jill Jill Jenkins (Inactive) added a comment - Sublime shows single tab space between field1&2 (lines15-end) but IGB is interpreting the tab as just a space. Replacing the whitespace between fields1&2 with space OR tab aligns the fields the same. There might be something with how IGB is interpreting that space therefore how it's displaying field14. If two tab spaces between fields 1&2 are used to align lines 15-6160 to 1-14, IGB correctly displays description.
            Jill Jill Jenkins (Inactive) made changes -
            Assignee Jill Jenkins [ jill ] Nowlan Freese [ nfreese ]
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            nfreese Nowlan Freese added a comment - - edited

            Do I need to do something for this issue? The bed file seems to be working on my system, field 14 is showing correctly.

            Show
            nfreese Nowlan Freese added a comment - - edited Do I need to do something for this issue? The bed file seems to be working on my system, field 14 is showing correctly.
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            Jill Jill Jenkins (Inactive) added a comment -

            I just wanted to bring it to your attention that I reached that point. Out of curiosity, did you drag and drop the bed file or reformatted file into IGB? There is a file that I reformatted a few lines of to show that it works in that format. Otherwise, I attached the screen shot of how the 'typical' bed file would look in IGB for me.

            Show
            Jill Jill Jenkins (Inactive) added a comment - I just wanted to bring it to your attention that I reached that point. Out of curiosity, did you drag and drop the bed file or reformatted file into IGB? There is a file that I reformatted a few lines of to show that it works in that format. Otherwise, I attached the screen shot of how the 'typical' bed file would look in IGB for me.
            nfreese Nowlan Freese made changes -
            Assignee Nowlan Freese [ nfreese ]
            nfreese Nowlan Freese made changes -
            Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
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            Jill Jill Jenkins (Inactive) added a comment - - edited

            Resolved, thanks to Nolan! The annots.xml file was pointing to the GFF file and not the BED file - no corrective formatting required.

            Show
            Jill Jill Jenkins (Inactive) added a comment - - edited Resolved, thanks to Nolan! The annots.xml file was pointing to the GFF file and not the BED file - no corrective formatting required.
            ann.loraine Ann Loraine made changes -
            Sprint Spring 2019 Sprint 2 [ 60 ] Spring 2019 Sprint 2, Spring 2019 Sprint 3 [ 60, 61 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            ann.loraine Ann Loraine made changes -
            Status Needs 1st Level Review [ 10005 ] Reviewing [ 10301 ]
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            ann.loraine Ann Loraine added a comment -

            Files in Dropbox folder don't reflect comments below.

            • annots.xml references C_albicans_WO-1_Jul_2010_refGene.bed.gz, which is not there
            • refGene should only be used for annotations obtained from UCSC database
            • there is a README.md file but no HEADER.md file
            Show
            ann.loraine Ann Loraine added a comment - Files in Dropbox folder don't reflect comments below. annots.xml references C_albicans_WO-1_Jul_2010_refGene.bed.gz, which is not there refGene should only be used for annotations obtained from UCSC database there is a README.md file but no HEADER.md file
            ann.loraine Ann Loraine made changes -
            Status Reviewing [ 10301 ] Open [ 1 ]
            ann.loraine Ann Loraine made changes -
            Assignee Jill Jenkins [ jill ]
            ann.loraine Ann Loraine made changes -
            Sprint Spring 2019 Sprint 2, Spring 2019 Sprint 3 [ 60, 61 ] Spring 2019 Sprint 2, Spring 2019 Sprint 3, Spring 2019 Sprint 4 [ 60, 61, 62 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
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            Jill Jill Jenkins (Inactive) added a comment - - edited
            • This issue is for the Dec 2013 assembly. The annots points to C_albicans_WO-1_Dec_2013.bed.gz
            • I show no _refgene uses in this directory
            • Other (C_albicans) assemblies only have README.md files. Should all assemblies have HEADER.md?
            Show
            Jill Jill Jenkins (Inactive) added a comment - - edited This issue is for the Dec 2013 assembly. The annots points to C_albicans_WO-1_Dec_2013.bed.gz I show no _refgene uses in this directory Other (C_albicans) assemblies only have README.md files. Should all assemblies have HEADER.md?
            Jill Jill Jenkins (Inactive) made changes -
            Status Open [ 1 ] In Progress [ 3 ]
            Jill Jill Jenkins (Inactive) made changes -
            Assignee Jill Jenkins [ jill ]
            Jill Jill Jenkins (Inactive) made changes -
            Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
            ann.loraine Ann Loraine made changes -
            Sprint Spring 2019 Sprint 2, Spring 2019 Sprint 3, Spring 2019 Sprint 4 [ 60, 61, 62 ] Spring 2019 Sprint 2, Spring 2019 Sprint 3, Spring 2019 Sprint 4, Spring 2019 Sprint 5 [ 60, 61, 62, 63 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            ann.loraine Ann Loraine made changes -
            Sprint Spring 2019 Sprint 2, Spring 2019 Sprint 3, Spring 2019 Sprint 4, Spring 2019 Sprint 5 [ 60, 61, 62, 63 ] Spring 2019 Sprint 2, Spring 2019 Sprint 3, Spring 2019 Sprint 4, Spring 2019 Sprint 5, Spring 2019 Sprint 6 [ 60, 61, 62, 63, 64 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            ann.loraine Ann Loraine made changes -
            Sprint Spring 2019 Sprint 2, Spring 2019 Sprint 3, Spring 2019 Sprint 4, Spring 2019 Sprint 5, Spring 2019 Sprint 6 [ 60, 61, 62, 63, 64 ] Spring 2019 Sprint 2, Spring 2019 Sprint 3, Spring 2019 Sprint 4, Spring 2019 Sprint 5 [ 60, 61, 62, 63 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked lower
            ann.loraine Ann Loraine made changes -
            Workflow Loraine Lab Workflow [ 18214 ] Fall 2019 Workflow Update [ 20712 ]
            ann.loraine Ann Loraine made changes -
            Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
            ann.loraine Ann Loraine made changes -
            Assignee Ann Loraine [ aloraine ]
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            ann.loraine Ann Loraine added a comment -

            Still to do:

            • Add HEADER.md summarizing where the files added to QL came from.
            Show
            ann.loraine Ann Loraine added a comment - Still to do: Add HEADER.md summarizing where the files added to QL came from.
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            ann.loraine Ann Loraine added a comment -

            Committed all files (except still-to-be-created HEADER.md file) to SVN repo.

            Show
            ann.loraine Ann Loraine added a comment - Committed all files (except still-to-be-created HEADER.md file) to SVN repo.
            ann.loraine Ann Loraine made changes -
            Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
            ann.loraine Ann Loraine made changes -
            Assignee Ann Loraine [ aloraine ]
            ann.loraine Ann Loraine made changes -
            Epic Link IGBF-1765 [ 17855 ]
            ann.loraine Ann Loraine made changes -
            Sprint Spring 2019 Sprint 2, Spring 2019 Sprint 3, Spring 2019 Sprint 4, Spring 2019 Sprint 5 [ 60, 61, 62, 63 ] Spring 2019 Sprint 2, Spring 2019 Sprint 3, Spring 2019 Sprint 4, Spring 2019 Sprint 5, Fall 2019 Sprint 2 [ 60, 61, 62, 63, 73 ]
            ann.loraine Ann Loraine made changes -
            Sprint Spring 2019 Sprint 2, Spring 2019 Sprint 3, Spring 2019 Sprint 4, Spring 2019 Sprint 5, Fall 2019 Sprint 2 [ 60, 61, 62, 63, 73 ] Spring 2019 Sprint 2, Spring 2019 Sprint 3, Spring 2019 Sprint 4, Spring 2019 Sprint 5, Fall 2019 Sprint 2, Fall 2019 Sprint 4 [ 60, 61, 62, 63, 73, 74 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            ann.loraine Ann Loraine made changes -
            Status To-Do [ 10305 ] In Progress [ 3 ]
            ann.loraine Ann Loraine made changes -
            Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
            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 ]
            ann.loraine Ann Loraine made changes -
            Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
            ann.loraine Ann Loraine made changes -
            Resolution Done [ 10000 ]
            Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
            ann.loraine Ann Loraine made changes -
            Workflow Fall 2019 Workflow Update [ 20712 ] Revised Fall 2019 Workflow Update [ 22123 ]

              People

              • Assignee:
                Unassigned
                Reporter:
                Jill Jill Jenkins (Inactive)
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                Watchers:
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                Dates

                • Created:
                  Updated:
                  Resolved: