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  1. IGB
  2. IGBF-3599

Investigate file types provided by UCSC REST

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          Situation: The UCSC REST endpoint provides many more track types than DAS. Some of them can be easily mapped to IGB's bed parser or a graph parser, but others we are unsure of.

          Task: List out the different track types being provided by UCSC REST and determine which tracks can be easily parsed by IGB.

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              relates to

              Task - A task that needs to be done. IGBF-3598 Implement logic to load data for BED file type

              • Major - Major loss of function.
              • Closed

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                nfreese Nowlan Freese added a comment - - edited
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                nfreese Nowlan Freese added a comment - - edited Example URL discussing the schema for repeatmasker: https://genome.ucsc.edu/cgi-bin/hgTrackUi?g=rmsk API schema for alligator track netGalGal6 https://api.genome.ucsc.edu/list/schema?genome=allMis1;track=netGalGal6 Data types found in tracks: http://genome.ucsc.edu/FAQ/FAQformat.html IGB File Formats: https://wiki.bioviz.org/confluence/display/igbman/File+Formats#:~:text=IGB%20supports%20partial%20data%20loading,indexed%20file%20and%20its%20index%20( .
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                nfreese Nowlan Freese added a comment -

                Google sheet link with track types and whether (I think) we can parse them in IGB: https://docs.google.com/spreadsheets/d/1epLMB2zPOjReiJ9L7-UcX8gCn52yIoquc4ufUrH0uS0/edit?usp=sharing

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                nfreese Nowlan Freese added a comment - Google sheet link with track types and whether (I think) we can parse them in IGB: https://docs.google.com/spreadsheets/d/1epLMB2zPOjReiJ9L7-UcX8gCn52yIoquc4ufUrH0uS0/edit?usp=sharing
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                jsirigin Jaya Sravani Sirigineedi (Inactive) added a comment -

                Looking into the file types mentioned in the above spreadsheet, investing a way on how to parse it, searching if there's any existing logic in code that might support it, and making notes on the findings.

                Show
                jsirigin Jaya Sravani Sirigineedi (Inactive) added a comment - Looking into the file types mentioned in the above spreadsheet, investing a way on how to parse it, searching if there's any existing logic in code that might support it, and making notes on the findings.
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                nfreese Nowlan Freese added a comment - - edited

                After discussion with Sravani we have decided the following.

                Create new tickets implementing:

                • narrowPeak > parse as narrowPeak
                • bigGenePred > parse as either bed or genePred
                • barChart > parse as bed or graph

                The following formats will require additional investigation, but we will not implement them as part of this epic:

                • chain
                • net
                • rmsk
                • wigMaf
                Show
                nfreese Nowlan Freese added a comment - - edited After discussion with Sravani we have decided the following. Create new tickets implementing: narrowPeak > parse as narrowPeak bigGenePred > parse as either bed or genePred barChart > parse as bed or graph The following formats will require additional investigation, but we will not implement them as part of this epic: chain net rmsk wigMaf
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                jsirigin Jaya Sravani Sirigineedi (Inactive) added a comment -

                Created tickets for the three file types (narrowPeak, bigGenePred, and barChart). Closing this ticket now and will start working on these tickets.

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                jsirigin Jaya Sravani Sirigineedi (Inactive) added a comment - Created tickets for the three file types (narrowPeak, bigGenePred, and barChart). Closing this ticket now and will start working on these tickets.

                  People

                  • Assignee:
                    jsirigin Jaya Sravani Sirigineedi (Inactive)
                    Reporter:
                    nfreese Nowlan Freese
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                    • Created:
                      Updated:
                      Resolved: