bin_by_bin/*-abundance.txt

[David Needham]

Dear Meren et al.,

I feel like this is a silly question, but I'm not figuring it out very quickly; maybe I missed the description online somewhere.

Can you define the *-abundance.txt values in the bin_by_bin directory?

I can see that it is closely related to the mean_coverage * total_length / number of reads in a sample. But that doesn't seem to be it. 

Thanks!

David

[A. Murat Eren]

Hi David,

It is not a silly question, but rather the result of poor documentation :( I apologize for that. I will put together something as soon as I have some time to describe each file in the summary output.

Best wishes,

--

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

--
Anvi'o Paper: https://peerj.com/articles/1319/
Project Page: http://merenlab.org/projects/anvio/
Code Repository: https://github.com/meren/anvio
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[mldi...@ucdavis.edu]

Hi,

Did this ever get resolved?  I'm also having a lot of trouble finding documentation on the precise differences between abundance, relative abundance, and percent recruitment across samples.

Thanks,

Megan

On Thursday, August 18, 2016 at 6:41:12 AM UTC-7, Meren wrote:

Hi David,

It is not a silly question, but rather the result of poor documentation :( I apologize for that. I will put together something as soon as I have some time to describe each file in the summary output.

Best wishes,

--

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

On Wed, Aug 17, 2016 at 8:28 PM, David Needham <dmne...@gmail.com> wrote:

Dear Meren et al.,

I feel like this is a silly question, but I'm not figuring it out very quickly; maybe I missed the description online somewhere.

Can you define the *-abundance.txt values in the bin_by_bin directory?

I can see that it is closely related to the mean_coverage * total_length / number of reads in a sample. But that doesn't seem to be it. 

Thanks!

David

--
Anvi'o Paper: https://peerj.com/articles/1319/
Project Page: http://merenlab.org/projects/anvio/
Code Repository: https://github.com/meren/anvio
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[David Needham]

Hi Megan, 

I think this will probably help, courtesy of Mike Lee: http://merenlab.org/2017/05/08/anvio-views/

Best,

David

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