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Original plan was to parse the mappings `RNAID -> TaxID` in https://github.com/ohnosequences/db.rna16s.assignments/, but since this is going to be required also in https://github.com/ohnosequences/db.…
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Given a set of left-right primers and read lengths we can extract the corresponding amplicon regions, compute which sequences collapse into one amplicon region, etc. Questions
1. Should all this be…
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From https://github.com/ohnosequences/db.rnacentral/issues/54
> Original plan was to parse the mappings RNAID -> TaxID in https://github.com/ohnosequences/db.rna16s.assignments/, but since this is go…
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RNACentral release 8 was [published on December, 2017](http://blog.rnacentral.org/2017/12/rnacentral-release-8.html).
A quick test showed that version 2.0 ---and probably 1.x, although that was not s…
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We need some code to convert the original tree from NCBI FTP to the custom format specified in #4.
Needs #4.
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https://github.com/RNAcentral/rnacentral-import-pipeline/pull/12 got merged recently.
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Each reference in the DB needs to be assigned to a set of nodes in the taxonomy tree from [ohnosequences/ncbitaxonomy](https://github.com/ohnosequences/ncbitaxonomy) repo. We may also compute the LCA …
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See https://github.com/ohnosequences/db.rna16s-paper-2017/issues/6#issuecomment-276719633. Using #68:
> As part of the pick 16S candidates step (or as a new step, I don't care much) we require that…
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From https://github.com/ohnosequences/db.rna16s-paper-2017/issues/6#issuecomment-276719633:
> build a 23S reference sequence database (taxonomy assignments are irrelevant here); we only need to do …
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1.1.0 was released without modifying the code in 1.1.0-RC1: https://github.com/ohnosequences/db.rna16s/compare/v1.1.0-RC1...v1.1.0, but we didn't run any data generation. We need to copy 1.1.0-RC1 fil…