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Ecological-and-Evolutionary-Genomics / eeg2016

Ecological and Evolutionary Genomics 2016
GNU General Public License v3.0
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Class Project selection #32

Closed CADNA closed 8 years ago

CADNA commented 8 years ago

I've got a couple class projects ideas, but I'm such a newbie I don't know what problems are hard and what are easy.

I really need to demultiplex inner tags though.

@rec3141 could I see your demultiplexing script you've used to date for pulling apart the variable length tag combos we use? What aspects of it merit improvement?

Another category of idea would be to analyze some aspect of our MinION, or perhaps a benchmark of MinION vs. MiSeq data on some sample/workflow.

rec3141 commented 8 years ago

Sometimes the only reason we do something hard is because we don't know how hard it is! But it gets done haha. I'll upload the script to github as soon as I can find it. What I wanted to do was build it into a BaseSpace app, which use a virtual machine framework called Docker. Getting the communication between the Docker instance and Basespace working was where I ran out of time/patience. The script should run on the command line in any case.

For the MinION vs. MiSeq comparison, an analysis of genome assembly quality using each platform individually and combined could be very interesting and not too difficult.