Relative abundance of OTUs in * file


This is probably a redundant question but I hope to have some confirmation. The data in * 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?


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


Hi Pat and Sarah,

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

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

i.e. ‘mothur >, count=.pick.count_table)’

Looking forward to your inputs. Thanks!

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

mothur >, 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 c__Actinobacteria 1 0.053719
4 o__Bifidobacteriales 1 0.053719
5 f__Bifidobacteriaceae 1 0.053719
6 g__Bifidobacterium 3 0.053719

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

Thanks for the quick reply!

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