Automated nucleotide position picking for oligotype convergence?

[dj.la...@gmail.com]

Hi,

I was wondering do you really manually deconstruct each oligotype by looking at individual entropy profiles in the html report? At least that's the impression I get from the tutorial and best practices guide. It's seems like a really tedious process or at least I've found it to be plus it has a lot of room for human error. I have a case where even after 6-7 rounds of oligotyping, the oligotypes haven't converged and keeping track of all the nucleotide positions which are shared between different oligotypes manually is becoming messy.

I was thinking of writing a script which would scan all the entropy files (OLIGO-REPRESENTATIVES/*_unique_entropy), look for values >0.5 (or any other suggestions) and automating the whole process in a way.

Are there maybe tools already for that or what would be the best way to go about this be? I'd appreciate any suggestions.

Thanks,
Dino

[A. Murat Eren]

http://www.nature.com/ismej/journal/v9/n4/full/ismej2014195a.html

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A. Murat Eren (meren)
http://merenlab.org :: gpg

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[dj.la...@gmail.com]

Thanks, but because the MED page mainly refers back to the oligotyping tutorial I figured somehow these were merged into just oligotyping at some point.

Nvm, found the decompose command, all fine!

On Tuesday, June 13, 2017 at 3:13:24 PM UTC+2, A. Murat Eren wrote:

http://www.nature.com/ismej/journal/v9/n4/full/ismej2014195a.html

--

A. Murat Eren (meren)
http://merenlab.org :: gpg

On Tue, Jun 13, 2017 at 7:54 AM, <dj.la...@gmail.com> wrote:

Hi,

I was wondering do you really manually deconstruct each oligotype by looking at individual entropy profiles in the html report? At least that's the impression I get from the tutorial and best practices guide. It's seems like a really tedious process or at least I've found it to be plus it has a lot of room for human error. I have a case where even after 6-7 rounds of oligotyping, the oligotypes haven't converged and keeping track of all the nucleotide positions which are shared between different oligotypes manually is becoming messy.

I was thinking of writing a script which would scan all the entropy files (OLIGO-REPRESENTATIVES/*_unique_entropy), look for values >0.5 (or any other suggestions) and automating the whole process in a way.

Are there maybe tools already for that or what would be the best way to go about this be? I'd appreciate any suggestions.

Thanks,
Dino

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