how to identify OTU distribution of each sample within a group

Hi all,

I’m wondering if there is any way to identify OTU distribution of each sample within a group?

Following SOP, the generated files of tax and tax.summary gave me total numbers of OTU of the group, but no information of each sample.

for instance,
OTU Size PHYLUM CLASS ORDER FAMILY GENUS
Otu0001 113118 Firmicutes(100) Bacilli(100) Lactobacillales(100) Lactobacillaceae(100) Lactobacillus(100)
Otu0002 99962 Actinobacteria(100) Actinobacteria(100) Micrococcales(100) Brevibacteriaceae(100) Brevibacterium(100)
Otu0003 99944 Firmicutes(100) Bacilli(100) Bacillales(100) Staphylococcaceae(100) Staphylococcus(100)

taxlevel rankID taxon daughterlevels total AFTERSCALD
0 0 Root 1 4955 4955
1 0.1 Bacteria 20 4955 4955
2 0.1.1 Acidobacteria 1 4 4
3 0.1.1.1 Blastocatellia 1 4 4

and I’m curious if there is a way that i can actually identify the distribution of OTU0003 among 10 samples for example, so that i can look more into the results of each individual sample.

Thank you in advance!

from the wiki of summary.tax, using count parameter of summary.tax should give me the distribution info of individual samples within the group, but it didn’t.

These data would be in the shared file generated by make.shared.

Pat

Thank you Pat! I’ve tried another way to see the data, allow me to explain and see if there is a better way to do it please.

mothur seems can read group details and show the distribution of OTUs among the group at certain level of file tree, e.g. \Users\XXX\Documents\samples, when i put data folder inside “samples” and name it as data, so the file tree would be \Users\XXX\Documents\samples\data. and the results would be only the total taxo summary of the group, rather than individual sample.

\Users\XXX\Documents\samples
taxlevel rankID taxon daughterlevels total S1 S2 S3 S4
0 0 Root 1 4955 1010 1345 1013 458
1 0.1 Bacteria 20 4955 1010 1345 1013 458
2 0.1.1 Acidobacteria 1 4 1 0 1 0
3 0.1.1.1 Blastocatellia 1 4 2 0 1 0

\Users\XXX\Documents\samples\data
taxlevel rankID taxon daughterlevels total DATA
0 0 Root 1 4955 4955
1 0.1 Bacteria 20 4955 4955
2 0.1.1 Acidobacteria 1 4 4
3 0.1.1.1 Blastocatellia 1 4 4

like above. in this way, it will give me detail of each sample in the taxonomy summary.

given sometime the dataset would be quite big and i would like to do it in a different hard drive. last night i tried to put all my data into a portable drive and ran mothur in it. but can’t set inputdir to the drive when make.file. the path was E:\Documents\mothur\samples.

wonder if any suggestion about it please? my C drive is only 100GB left and my data from Illumina is 20GB after decompressed.

many thanks