Genome abundance

[Aditya Bandla]

Hi

I have been trying to make sense of "abundance" values for each genome bin, across samples in the interactive view

From this post, http://merenlab.org/2017/05/08/anvio-views/#abundance

Is it correct to infer that the abundance value for a particular genome bin in a particular sample, represents the mean abundance of that genome bin in that sample?

Regards,

Aditya

[Mike Lee]

Hi there, Aditya,

The 'abundance' when considering a genome/bin would be similar to when considering a contig, meaning, the abundance of a bin is the bin's mean coverage divided by the sample's overall mean coverage. 

So if the mean coverage of all the contigs in your sample is 5, and the mean coverage of Bin_A is 10, then the 'abundance' for Bin_A would be 10/5 = 2. 

Does that make sense? 

You can check this out by looking in the summary output bins_across_samples directory. If you look at the mean_coverage.txt file, you can take the mean coverage of the bins from a specific sample, then divide one of the bins by that overall mean coverage, it should be close to what you see for that bin in that sample in the abundance.txt file

-mike 

--
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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[Aditya Bandla]

Hi Mike

Thanks for the reply! I could understand the first part, very clear

However, the manual check that you suggest is a bit confusing. It might be right if all the contigs in the database have been clustered into bins. In most cases, only a subset of contigs are clustered into bins. In that case, is the overall mean coverage per samples, calculated across all contigs (binned and unbinned) or just the contigs that have been binned?

Aditya

On Tuesday, August 1, 2017 at 12:37:32 AM UTC+8, Mike Lee wrote:

Hi there, Aditya,

The 'abundance' when considering a genome/bin would be similar to when considering a contig, meaning, the abundance of a bin is the bin's mean coverage divided by the sample's overall mean coverage. 

So if the mean coverage of all the contigs in your sample is 5, and the mean coverage of Bin_A is 10, then the 'abundance' for Bin_A would be 10/5 = 2. 

Does that make sense? 

You can check this out by looking in the summary output bins_across_samples directory. If you look at the mean_coverage.txt file, you can take the mean coverage of the bins from a specific sample, then divide one of the bins by that overall mean coverage, it should be close to what you see for that bin in that sample in the abundance.txt file

-mike 

On Mon, Jul 31, 2017 at 11:31 AM, Aditya Bandla <aditya...@gmail.com> wrote:

Hi

I have been trying to make sense of "abundance" values for each genome bin, across samples in the interactive view

From this post, http://merenlab.org/2017/05/08/anvio-views/#abundance

Is it correct to infer that the abundance value for a particular genome bin in a particular sample, represents the mean abundance of that genome bin in that sample?

Regards,

Aditya

--
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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[Mike Lee]

Ah, sorry for the confusion. I absolutely tested that real quick on a dataset where I have everything in some sort of bin. I am pretty sure the overall mean abundance of a sample includes all contigs (those not binned as well as those that are), so checking the way i just suggested wouldn't work like that if you have unbinned contigs not included in the summary. 

Sorry for the added confusion! 

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