Wednesday, October 10, 2012

5 rules of pollex about genomics

Ewan Birney wrote a post on 10 rules of thumb in genomics almost a year ago. It is very true and will probably remain like that for "some" more time. Few more rules of pollex in no particular order

  1. Trust the box, but know that the box is not perfect. Many steps in genomics require us to trust a black box, be it genome assemblers (that has way too much code to inspect) or simple read trimming programs. Moreover, manual verification of all data is impossible due to the shear size of the data.
  2. Default values are not always the best values.All most all bioinformatics tool have half a dozen parameters which have some default value set in them. However, these default values might not be suitable for your data or analysis. Not being aware of the various options can have unpredictable results.
  3. New programs keep coming up everyday.Unless the robustness of these programs has been tested by independent users, using these can be tricky.
  4. Changes in technology are very fast. Methods keep getting better all the time and can add more to an analysis. A bit contradictory to the previous point.
  5. Validate your results by various other methods. Artifacts are not unheard of in NGS data, and require validation from other methods.

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