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Methods (and dataflow for Laura's education) #181

Closed lauradoepker closed 6 years ago

lauradoepker commented 7 years ago

We should nail down the methods for our current (and previous) CFT deployment.

The methods document is here: https://docs.google.com/document/d/1xjxcEun_vqOJibc-NrhleP0Jqskda2MIuaqXpc4_Ias/edit

In order for me to be more effective in our group, I'll need @metasoarous to walk me through what happens on his end beginning from the partis output provided by @psathyrella . This will help me become more helpful with pipeline tinkering. At the same time, this will also help us fill out the post-partis methods section for future papers. @metasoarous can we do this once you're back in Seattle?

@psathyrella has already filled out his methods portion, but since there have been partis updates recently, maybe a methods update is also in order.

Sweet publication storms are brewing!

psathyrella commented 7 years ago

ok I edited, the only change was allele finding is on by default now, so it's just all default options.

I realize my sections kinda short, I'm happy to add more but would want some direction on which details, if so.

metasoarous commented 7 years ago

@lauranoges and I are going to start working on this remotely, sometime soon.

metasoarous commented 6 years ago

@lauranoges Do you think we're good to close this issue now that you have written up your methods?

lauradoepker commented 6 years ago

Yes we're good.