Uploaded image for project: 'IGB'
  1. IGB
  2. IGBF-3245

Investigate: Why do coverage graphs look different?

        Details

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

          Description

          The new time course dataset from Mark Johnson lab was generated using a different sequencing protocol - paired-end strand specific versus paired-end non-strand specific as in earlier sequencing runs.

          For some reason, the coverage graphs we made look different, with different patterns of peaks and valleys.

          For an example, see:

          https://bitbucket.org/hotpollen/splicing-analysis/src/main/GenomeBrowserImages/TimeCourseVsOlderData-CoverageGraphProfileDifference.png

          For this task, please investigate why this is the case.

          For your reference, coverage graph generation code is here:

          https://bitbucket.org/hotpollen/splicing-analysis/src/main/src/bamCoverage.sh
          in

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-3244 Run rnaseq pipeline on mark-2022-timeseries

              • Major - Major loss of function.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                ann.loraine Ann Loraine created issue -
                ann.loraine Ann Loraine made changes -
                Field Original Value New Value
                Epic Link IGBF-2993 [ 21429 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-3244 [ IGBF-3244 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 3 2023 Feb 1 [ 163 ]

                  People

                  • Assignee:
                    Unassigned
                    Reporter:
                    ann.loraine Ann Loraine
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    1 Start watching this issue

                    Dates

                    • Created:
                      Updated: