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ohsu-comp-bio / tcrseq_normalization

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T-Cell Concentration and Coverage Depth #10

Open weshorton opened 8 years ago

weshorton commented 8 years ago

Summary

We need a minimum of 30x coverage in order to confidently identify unique VDJ sequences as truly unique. In addition, we need to ensure that this coverage amount can be met for all samples, even though we have large variation in the concentration of T-cells within these samples. We assume that a highly diverse sample will have a correspondingly lower average read depth, but need to determine the correlation between initial T-cell concentration and read depth.

Significance

Adequate coverage is essential for accurate results.

To Do

  1. Obtain flow data for DNA160107 sequencing run
    • assignee - DM
  2. Verify MiXCR output accuracy (#11)
    • assignee - WH
  3. Scripts to compare flow data and clonotype data for read depth correlation (Knitr)
    • assignee - WH
  4. Narrative of problem, experiment, results, conclusions (Knitr)
    • assignee - BD

      Approach

  5. Complete MiXCR Issue
  6. Linear regression of flow concentration vs. depth of coverage
    • predictor - concentration
    • response - depth of coverage
  7. Compile into knitr narrative
weshorton commented 8 years ago

To Do.

  1. Make milestone
  2. Separate above to do's into individual issues.