Relative abundance (%) of each OTU in multiple samples.

Question

[maha_2447]

Hi,

I am new to dealing with sequencing data. please explain or help me understand following:

1. I have done sequencing of 8 samples(triplicates) from fermentation reactors. I want to represent my data and discuss it on the basis of OTUs I am trying to understand what are OTUs and how I can use the values provided to explain my results and relate them to microbial Diversity. Please guide me in this regard.

I read this paper: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030440 This supplementary table (https://doi.org/10.1371/journal.pone.0030440.s005 (DOC) that uses OTUs to calculate relative abundance. I want to learn what does relative abundance tells me in this case and how do I calculate it in my case.

as I am a beginner so I am even confused what to ask and where to start. please guide me if you can spare some time!

Best regards

[Kristoffer Vitting-Seerup]

Could you clarify what type of sequencing and what your aims are? (I'm guessing RNA-seq and gene expression analysis but it's not clear)

Answer 1

[Istvan Albert]

Better late than never ;-)

In the paper that you cite the relative OTU abundance means what percent of each OTU was detected in the sample.

The percents are relative to the other OTUs in the sample, 10% OTU1, 50% OTU2, all add up to 100%.

The important detail to remember here is that across samples you would not know how much of that OTU is there on an absolute scale.

10% OTU1 in sample A and 99% OTU1 in the other sample B does not mean that sample B has more of the OTU1 than sample A. On an absolute scale sample, A could have more, it only has less relative to other OTUs that are present.

To calculate the relative abundance sum up all counts and divide each count with the sum, same way that you would compute percents.

10, 10, 30 -> 10/50, 10/50, 30/50 -> 20%, 20%, 60%