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veg / flea-pipeline

A pipeline for long-read sequencing data.
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poly-A trimming needs to check for empty sequences #34

Closed kemaleren closed 9 years ago

kemaleren commented 9 years ago

If the entire sequence is poly-A or poly-T, it should get dropped.

kemaleren commented 9 years ago

It looks like there can by poly-As and poly-Ts both at the beginning and at the end. HMM will need to be more sophisticated.

kemaleren commented 9 years ago

Plan for now: trim heads and tails, both for As and Ts. Then filter sequences with runs of length >n As or Ts.