Question: Rarefaction curve at different sequencing depths
gravatar for bioinfo
3.3 years ago by
bioinfo790 wrote:

I have a table which contains the number of different taxa in different samples from metagenomics data.

Sample      seq_depth       16S counts   taxa1     taxa2    taxa3    taxa4
   1           55000            230        30        39      40       12
   2           72000            300        23        53      20       64
   3           137000           540        20        135     12       94
   4           84000            250        48        37      102      74

I want to create a rarefaction curve based on that. What's the best way to do that? I have looked at the Qiime but the script doesn't take into consideration of the column B (Seq_depth) to create the rarefaction curve (we can ignore column C - 16S counts here). I was wondering when we use the input OTU table in Qiime do we provide sequencing depth info at all in a column or it just take Sample id and taxa columns?

In addition, if I want to create a new taxa counts table at an even sequencing depths (e.g. 50000) or at even 16S counts (e.g. 230) for all 4 samples. Is there a strategy to do that?

ADD COMMENTlink modified 3.3 years ago by Istvan Albert ♦♦ 85k • written 3.3 years ago by bioinfo790

Did you try QIIME's scripts for rarefaction?

ADD REPLYlink written 3.3 years ago by Bioinformatics_NewComer320
gravatar for Istvan Albert
3.3 years ago by
Istvan Albert ♦♦ 85k
University Park, USA
Istvan Albert ♦♦ 85k wrote:

The point of the rarefaction curve is to estimate the species richness as a function of sampling (sequencing depth). A higher sequencing depth will only make the curve go on longer but otherwise is comparable to a lower sequencing depth curve for the regions that both cover.

Cut the last values off if you really want both to go the same distance - though it would make no sense to do so - the whole point of the rarefaction is to assess how well the sampling covers the actual richness. There is little information to be had from tossing that.

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by Istvan Albert ♦♦ 85k
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