Relative abundance

[Julius Nweze]

Please, how can I get a relative abundance from anvio that is comparable to the relative abundance from amplicon sequence data? I am trying to compare the relative abundance from my anvio-7 MAG summary and my amplicon sequence data (both from the same sample source).

[Julius Nweze]

How can I get the relative abundance of MAGs within a sample (not across all samples)? Your help will be highly appreciated.

[Iva Veseli]

Hi Julius,

Have you tried looking at the bin_by_bin subdirectory from the output of ansi-summarize? https://anvio.org/help/7/artifacts/summary/

I think that should have the coverage data of each bin in each sample, from which you could calculate relative abundance.

Iva

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Iva Veseli (she/her)
Graduate Student, Meren Lab
Biophysical Sciences Program
University of Chicago

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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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[Julius Nweze]

Thanks for your reply.

Can I calculate it thus: Relative abundance = (mean coverage x reads length)/Total number of reads mapped to a sample?

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Nweze Julius Eyiuche

Biology Centre CAS
Soil and Water Infrastructure
Na Sádkách 702/7
370 05 České Budějovice
Czech Republic
Phone Number: +420777326352
E-mail: julius...@bc.cas.cz or julipe...@gmail.com
Skype username: live:julipeale2001

[Julius Nweze]

I am recalculating the relative abundance of my MAGs within a sample (earlier calculated it across the sample from anvio), and I have the mean coverage, MAG read length, percent recruitment and the total reads mapped in each sample. So, I am wondering how I can calculate the relative abundance within a sample. I have searched the literature but cannot find any info except "the number of reads mapped to a MAG divided by the total number of reads mapped to the corresponding sample."

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Nweze Julius Eyiuche

Currently, a Guest Scientist at Max Planck Institute of Terrestrial Microbiology in Marburg, Germany

A PhD Student at the Biology Centre CAS, Soil and Water Infrastructure, Na Sádkách 702/7, 370 05 České Budějovice, Czech Republic

Area of Specialization: Studying microbial communities and host-microbiome interactions using stable-isotope coupled meta-omics techniques