Question: How to calculate sequencing depth for 16S amplicon sequencing
0
gravatar for sifujio
5.2 years ago by
sifujio0
sifujio0 wrote:

Hi all, I would like to know how can I can calculate sequencing depth for amplicon sequencing.

I am conducting a microbial survey sequencing 16S rRNA´s V3-V4 region which yields an amplicon of ~450 pb. So for each sample I have a mixture of different amplicon size (around ~450pb) for each bacteria´s 16S that got amplified with the primers I used. 

I would like to use the The Lander / Waterman equation C=NL/G, but since I am not sequencing a whole genome but a set of unknown quantity of bacteria´s 16S, I don´t know what number to put in.  I am actually not even sure if it´s possible to calculate it, at least with that formula.. 

Please help, Cheers

ADD COMMENTlink modified 5.2 years ago by mikhail.shugay3.4k • written 5.2 years ago by sifujio0
3
gravatar for mikhail.shugay
5.2 years ago by
mikhail.shugay3.4k
Czech Republic, Brno, CEITEC
mikhail.shugay3.4k wrote:

Read coverage and organism abundance will interfere in such setting. I would recommend to focus rather on sample diversity metrics (see http://www.pnas.org/content/108/Supplement_1/4516.full.pdf+html ).

ADD COMMENTlink written 5.2 years ago by mikhail.shugay3.4k
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