Hi all,
I am using QIIME to analyse my 16S metagenomic sample.
I am going to compare the bacterial community of 2 group of sample and each group composed of 10 sets of samples
I have merged, trimmed and filtered my sequences and the no. of read for my 10 samples are:
Group 1: 88322, 131727, 150013, 169207, 177499, 193288, 197006, 200491, 201732, 229860
Group 2: 115444, 127776, 172511, 172573, 179295, 181659, 186582, 200619, 201387, 212047
I have subsample the reads to multiple rarefaction (sample size from 1000 to 88000 with step size of 2000) to calculate the alpha diversity with parallel_multiple_rarefactions.
I am going to use the jackknifed_beta_diversity to see if there is difference between 2 group of samples. Unlike alpha diversity, it seems that only a single depth is allowed to compute the beta diversity. I would like to ask what is the best sequence depth for compute the beta diversity and plot the principal coordinates analysis for these sets of data ? Between, is it a good idea to remove the data with only 88322 reads which is relative fewer reads?
Thanks for answering the long question.
I am using QIIME to analyse my 16S metagenomic sample.
I am going to compare the bacterial community of 2 group of sample and each group composed of 10 sets of samples
I have merged, trimmed and filtered my sequences and the no. of read for my 10 samples are:
Group 1: 88322, 131727, 150013, 169207, 177499, 193288, 197006, 200491, 201732, 229860
Group 2: 115444, 127776, 172511, 172573, 179295, 181659, 186582, 200619, 201387, 212047
I have subsample the reads to multiple rarefaction (sample size from 1000 to 88000 with step size of 2000) to calculate the alpha diversity with parallel_multiple_rarefactions.
I am going to use the jackknifed_beta_diversity to see if there is difference between 2 group of samples. Unlike alpha diversity, it seems that only a single depth is allowed to compute the beta diversity. I would like to ask what is the best sequence depth for compute the beta diversity and plot the principal coordinates analysis for these sets of data ? Between, is it a good idea to remove the data with only 88322 reads which is relative fewer reads?
Thanks for answering the long question.
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