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  1. IGB
  2. IGBF-2538

Support CSI tabix index for very large genomes

        Details

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

          Description

          Larger genomes, e.g., bread wheat, cannot be indexed using .bai (BAM) or .tbi (tabix) files due to size.

          There is an alternative type of index called "csi" that can be used instead. It does not have the same size limitation.

          See: https://www.biostars.org/p/111984/

          For this new feature, enable IGB to support partial data loading of files indexed using tabix -C (which creates a .csi index instead of a .tbi index).

          See attached for example BED file with csi index.

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-2333 Add wheat genome to IGB quickload system

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-2548 Investigate: Why do wheat gene models fail to load

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3409 Fix wheat genome files and documentation

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

              Task - A task that needs to be done. IGBF-2333 Add wheat genome to IGB quickload system

              • Major - Major loss of function.
              • Closed

                Activity

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                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-2333 [ IGBF-2333 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Attachment T_aestivum_Aug_2018.bed.gz [ 14874 ]
                Attachment T_aestivum_Aug_2018.bed.gz.csi [ 14875 ]
                ann.loraine Ann Loraine made changes -
                Description Larger genomes, e.g., bread wheat, cannot be indexed using .bai (BAM) or .tbi (tabix) files due to size.

                There is an alternative type of index called "csi" that can be used instead. It does not have the same size limitation.

                See: https://www.biostars.org/p/111984/

                For this new feature, enable IGB to support partial data loading of files indexed using tabix with the -C option.

                See attached for example BED file with csi index.

                		Larger genomes, e.g., bread wheat, cannot be indexed using .bai (BAM) or .tbi (tabix) files due to size.

                There is an alternative type of index called "csi" that can be used instead. It does not have the same size limitation.

                See: https://www.biostars.org/p/111984/

                For this new feature, enable IGB to support partial data loading of files indexed using tabix -C (which creates a .csi index instead of a .tbi index).

                See attached for example BED file with csi index.

                ann.loraine Ann Loraine made changes -
                Summary Support CSI index for BAM and bgzip (tabix) files Support CSI index for tabix-indexed files
                ann.loraine Ann Loraine made changes -
                Sprint Fall 2: 28 Sep - 9 Oct [ 104 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-2333 [ IGBF-2333 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-2548 [ IGBF-2548 ]
                ann.loraine Ann Loraine made changes -
                Summary Support CSI index for tabix-indexed files Support CSI tabix index for very large genomes
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Rank Ranked lower
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-3409 [ IGBF-3409 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher

                  People

                  • Assignee:
                    Unassigned
                    Reporter:
                    ann.loraine Ann Loraine
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                    Dates

                    • Created:
                      Updated: