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  1. IGB
  2. IGBF-4299

Hunting for read depth in M6A sites of interest

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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: To look at how many reads align in 3' UTR regions of interest mentioned by Kausik.

          Rob's prevailing thought: No reads align to these areas. Prove him wrong.

          1. Get file from Kausik's email with the gene of interest
          2. Find relevant reference annotation (GFF, GTF, refflat file, bed) that contains the gene name.
          3. Within this file, identify the coordinates for the 3'UTR
          4. Get coordinates for m6A sites related to this gene.
          5. Check how many reads for these sites and for the 3' UTR in general.
          6. Repeat for each gene.
          7. Repeat for each of the 10 files (Ring, troph, Schitz, etc)

          To figure out how to get the depth of reads using samtools.
          Can it all be done in Python but we use the samtools.

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                • Assignee:
                  bbendick Brandon Bendickson
                  Reporter:
                  robofjoy Robert Reid
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                    Updated:
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