Relative abundance of OTUs in *.cons.tax.summary file

Theory behind mothur
1

Hi,

This is probably a redundant question but I hope to have some confirmation. The data in *.cons.tax.summary file shows the number of otu categorized to each taxon, and does not include the relative abundance of each otu. Am I right? If I want that relative abundance data of otu for each group, I have to look at the shared file?

Thanks,
Soon

2

Correct. There’s also a sequence-based summary file from classify.seqs.

pat

3

Hi Pat and Sarah,

I am also looking at getting a *.cons.tax.summary file equivalent for sequence abundance rather than OTU abundance.

Could I achieve it through the summary.tax command with the *.wang.pick.taxonomy and *.pick.count_table files, generated after remove.lineage, as input files?

i.e. ‘mothur > summary.tax(taxonomy=.wang.pick.taxonomy, count=.pick.count_table)’

Looking forward to your inputs. Thanks!

4

Mothur will output the relative abundances instead of the raw abundances for you using the relabund parameter.

mothur > summary.tax(taxonomy=abrecovery.gg.wang.taxonomy, relabund=t)

taxlevel rankID taxon daughterlevels total
0 0 Root 1 1.000000
1 0.1 k__Bacteria 5 1.000000
2 0.1.1 p__Actinobacteria 1 0.053719
3 0.1.1.1 c__Actinobacteria 1 0.053719
4 0.1.1.1.1 o__Bifidobacteriales 1 0.053719
5 0.1.1.1.1.1 f__Bifidobacteriaceae 1 0.053719
6 0.1.1.1.1.1.1 g__Bifidobacterium 3 0.053719
…

The classify.seqs command has the relabund parameter as well.

5

Thanks for the quick reply!

Just a quick update - I tried the command ‘mothur > summary.tax(taxonomy=.wang.pick.taxonomy, count=.pick.count_table)’ and it worked too! But good to know that there is an alternative using the command you have provided :smiley: