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  1. IGB
  2. IGBF-4321

IGB visualizations of 3'UTR regions!

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

          GOAL: Use IGB to look at the 3'UTR regions in 27 genes that Kausik cares about.

          Need to see the pilups in general.
          And then the variants at some m6A sites that Brandon cares about.

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              robofjoy Robert Reid added a comment -

              This worked out GREAT !!!!!!

              This might be a great case study as to why to use IGB to look at data. Had we done this sooner, it would have saved us a bunch of pointless analyses!

              https://docs.google.com/presentation/d/1Jj1xEh6ZZpvSubwsB4kCsFYGVKcBUOjfmRi3Yq7OQdg/edit?usp=sharing

              Summary of this:
              Basically, we were hunting for mutations in the 3'UTR regions.
              We were not finding much.
              Upon loading the data into IGB, I was able to pull up the bedgraphs and show that most of the reads are aligning in the gene regions (this technique is Dart-Seq, not Rna-seq).
              Few to no reads in the 3'UTR regions!
              Mystery solved thanks to IGB.

              Case closed.
              Hopefully the end of our chapter with Kausik.

              I SHOULD add gene annotations to the result. That could be a new ticket.

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              robofjoy Robert Reid added a comment - This worked out GREAT !!!!!! This might be a great case study as to why to use IGB to look at data. Had we done this sooner, it would have saved us a bunch of pointless analyses! https://docs.google.com/presentation/d/1Jj1xEh6ZZpvSubwsB4kCsFYGVKcBUOjfmRi3Yq7OQdg/edit?usp=sharing Summary of this: Basically, we were hunting for mutations in the 3'UTR regions. We were not finding much. Upon loading the data into IGB, I was able to pull up the bedgraphs and show that most of the reads are aligning in the gene regions (this technique is Dart-Seq, not Rna-seq). Few to no reads in the 3'UTR regions! Mystery solved thanks to IGB. Case closed. Hopefully the end of our chapter with Kausik. I SHOULD add gene annotations to the result. That could be a new ticket.

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                • Assignee:
                  robofjoy Robert Reid
                  Reporter:
                  robofjoy Robert Reid
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                    Updated:
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