Update options in examples

Issue #30 resolved
Former user created an issue

Unless I'm missing something, I think maybe the examples have deprecated options (both here and in the repo)?

I think it's just that --clean needs to be removed, and the miseq pairseq command needs --f swapped for --1f.

Comments (5)

  1. Jason Vander Heiden

    Sorry, I seem to have missed this issue. This was right after my foot surgery, so I blame morphine, instead of myself!

    We emailed about updated docs a bit ago. Did the new docs solve this issue for you?

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