Compute basic OTU table statistics, rarefy and summarize OTU tables by taxa using miccaΒΆ
Note
This tutorial requires Single-end sequencing to be done.
The command tablestats reports a sample summary, an OTU summary and the rarefaction curves for the input OTU table:
micca tablestats -i otutable.txt -o tablestats
Inspecting the file tablestats/tablestats_samplesumm.txt
you can
see that the less abundant sample contains 9053 reads:
Sample Depth NOTU NSingle
Mw_03 9053 716 142
Mw_02 9947 760 166
Mw_12 10843 792 168
... ... ... ...
Note
Rarefaction curves can be inspected through
tablestats/tablestats_rarecurve.txt
and
tablestats/tablestats_rarecurve_plot.png
.
To compare different samples, the OTU table must be subsampled
(rarefied)
using the command tablerare. In this case we are
interested in rarefy the table with the depth of the less abundant
sample (Mw_03
):
micca tablerare -i otutable.txt -o otutable_rare.txt -d 9053
Now we can summarize communities by their taxonomic composition. The
tabletotax creates in the output directory a table for
each taxonomic level (taxtable1.txt
, ..., taxtableN.txt
). OTU
counts are summed together if they have the same taxonomy at the
considered level.
micca tabletotax -i otutable_rare.txt -t taxa.txt -o taxtables
Finally, we can generate a relative abundance bar plot from generated taxa tables, using the command tablebar. In this case only the bar plot relative to the taxonomy level 2 (phylum) will be generated:
micca tablebar -i taxtables/taxtable2.txt -o taxtables/taxtable2.png