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  1. IGB
  2. IGBF-4029

Investigate GFF file from NCBI not loading in IGB

        Details

        • Type: Improvement
        • Status: To-Do (View Workflow)
        • Priority: Major
        • Resolution: Unresolved
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          Situation: NCBI has many genomes and annotations that are useful to IGB users. Gene annotations are provided as a GFF or GTF file. The GFF (have not tested GTF) file does not currently load correctly in IGB.

          Task: Investigate why the NCBI GFF/GTF file is not loading correctly in IGB.

          To reproduce the issue:

          1. In a web browser:
          2. Go to https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_000328365.1/
          3. Click Download
          4. Select file types > Genome sequences (FASTA), Annotation features (GTF), and Annotation features (GFF)
          5. Click Download
          6. Unzip the ncbi_dataset.zip file
          7. In IGB:
          8. Click File > Open Genome from File...
          9. Select Reference Sequence > Browse...
          10. Select the GCA_000328365.1_Capca1_genomic.fna file in the unzipped ncbi_dataset folder
          11. Click OK
          12. Select File > Open File...
          13. Select the genomic.gff file in the unzipped ncbi_dataset folder
          14. Click Open
          15. Note the errors in the IGB Log

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-4002 Fix GFF null pointer exception when FASTA included

              • Major - Major loss of function.
              • Closed

                Activity

                  People

                  • Assignee:
                    Unassigned
                    Reporter:
                    nfreese Nowlan Freese
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                    Dates

                    • Created:
                      Updated: