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  1. IGB
  2. IGBF-1546

Add American eel genome

        Details

        • Story Points:
          1
        • Sprint:
          Spring 2019 Sprint 2, Spring 2019 Sprint 3, Spring 2019 Sprint 4, Spring 2019 Sprint 5

          Description

          Add Anguilla rostrata (American eel) genome to IGB.

          Fasta sequence and gff annotation can be found at dryad .

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              relates to

              Bug - A problem which impairs or prevents the functions of the product. HELP-319 Investigate why NCBI GFF files will not open

              • Major - Major loss of function.
              • To-Do

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                Jill Jill Jenkins (Inactive) added a comment - - edited
                • 'A_rostrata' no longer appears in my local IGB
                • Currently hosted annotations provided by Dryad, no additional functional annotations are available
                • Nowlan and I changed load mode to 'Visible'; per Nowlan, 'Manual' also works, we found this helps with lag; we could remove the annotation-free scaffolds also...
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                Jill Jill Jenkins (Inactive) added a comment - - edited 'A_rostrata' no longer appears in my local IGB Currently hosted annotations provided by Dryad, no additional functional annotations are available Nowlan and I changed load mode to 'Visible'; per Nowlan, 'Manual' also works, we found this helps with lag; we could remove the annotation-free scaffolds also...
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                ann.loraine Ann Loraine added a comment - - edited
                • I'm not sure why 'A_rostrata' still appears. Need to investigate.
                • BED file lacks functional annotations. Need to investigate: Can we add functional annotations from GFF files available from Dryad?
                • The large number of scaffolds is slowing down initial loading of the gene models. Need to investigate: Can we remove some of the smaller scaffolds that lack annotations on them? This might help.
                • IGB needs to a better job of supporting extremely fragmented assemblies with large numbers of scaffolds - like this one. To-Do: Create a Jira ticket to improve data loading for highly fragmented genomes such as this.
                • Note: I have made edits to annots.xml, HEADER.md. This is not a UCSC genome, so requires custom editing.
                Show
                ann.loraine Ann Loraine added a comment - - edited I'm not sure why 'A_rostrata' still appears. Need to investigate. BED file lacks functional annotations. Need to investigate: Can we add functional annotations from GFF files available from Dryad? The large number of scaffolds is slowing down initial loading of the gene models. Need to investigate: Can we remove some of the smaller scaffolds that lack annotations on them? This might help. IGB needs to a better job of supporting extremely fragmented assemblies with large numbers of scaffolds - like this one. To-Do: Create a Jira ticket to improve data loading for highly fragmented genomes such as this. Note: I have made edits to annots.xml, HEADER.md. This is not a UCSC genome, so requires custom editing.
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                Jill Jill Jenkins (Inactive) added a comment -

                Appended species.txt with Anguilla rostrata. Species dropdown on main screen still shows 'A_rostrata' - is this related to updating the species.txt that is packaged w/ IGB?

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                Jill Jill Jenkins (Inactive) added a comment - Appended species.txt with Anguilla rostrata. Species dropdown on main screen still shows 'A_rostrata' - is this related to updating the species.txt that is packaged w/ IGB?
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                Jill Jill Jenkins (Inactive) added a comment - - edited

                Added to Dropbox. IGB lags when Load Mode is set to "Whole Sequence" ( >80k scaffolds to parse). Workaround is setting Load Hint to "Manual" - but user would have to select drop down arrow from Available Data window. It's functional, but is it acceptable?

                Show
                Jill Jill Jenkins (Inactive) added a comment - - edited Added to Dropbox. IGB lags when Load Mode is set to "Whole Sequence" ( >80k scaffolds to parse). Workaround is setting Load Hint to "Manual" - but user would have to select drop down arrow from Available Data window. It's functional, but is it acceptable?

                  People

                  • Assignee:
                    Jill Jill Jenkins (Inactive)
                    Reporter:
                    nfreese Nowlan Freese
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                    • Created:
                      Updated:
                      Resolved: