update the reference DB section

ohnosequences / mg7

Configurable and scalable 16S metagenomics data analysis

https://goo.gl/y3rZFD

GNU Affero General Public License v3.0

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Closed eparejatobes closed 8 years ago

eparejatobes commented 8 years ago

Since the preprint this has significantly changed (and improved!). We need to

[x] describe (and cite) the original data source, RNACentral
[x] explain what kind of sequences are considered 16S
[x] how redundant assignments are collapsed
[x] our strategy for identifying and discarding wrong assignments
[x] how all this can be re-used for any subset of RNACentral, like for example 18S

eparejatobes commented 8 years ago

cc @rtobes @marina-manrique

eparejatobes commented 8 years ago

See ohnosequences/db.rna16s#32

eparejatobes commented 8 years ago

Please @marina-manrique @rtobes check this. I do think we should do a figure for what we consider a wrong assignment, and how are we discarding them.

rtobes commented 8 years ago

I am working in the section 16S-DB7 Reference Database Construction because it is not easy to understand. I am preparing a figure about it.

eparejatobes commented 8 years ago

@rtobes fixed everything in 094deab, thank you!

eparejatobes commented 8 years ago

If everyone's OK, I'd rather merge this and do the figure in a separate branch.

rtobes commented 8 years ago

OK for a new branch for the figure about the DB construction