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benjjneb / dada2

Accurate sample inference from amplicon data with single nucleotide resolution
http://benjjneb.github.io/dada2/
GNU Lesser General Public License v3.0
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combining the seqtab and taxa tables #774

Closed ganiatgithub closed 5 years ago

ganiatgithub commented 5 years ago

Hi,

I want to investigate the relative abundance of 5 genera, over 5 time points. I've adopted the dada2 tutorial to analyze my own data, and have generated the seqtab.nochim (5 rows, 3587 cols) and also taxa (3587 rows, 6 cols).

Intuitively I wish to obtain a table that contains information from both seqtab.nochim and taxa, how can I do that?

Alternatively, is there a way to select only 5 genera over 5 time points, and plot the relative abundance?

Kind regards.

benjjneb commented 5 years ago

Intuitively I wish to obtain a table that contains information from both seqtab.nochim and taxa, how can I do that?

I think cbind(seqtab.nochim, taxtab) will do it.

Alternatively, is there a way to select only 5 genera over 5 time points, and plot the relative abundance?

Yes, lots of ways to do that in R. What is your familiarity with working in R? Whether familiar or not, you ay want to look into the phyloseq package which has been built to help do the analysis of microbiome data (that dada2 package is focused on turning the bioinformatics of processing the raw sequencing data).