Alpha diversity: rarefaction file generation

Commands in mothur
1

Dear all,

I have just started using mothur (in Windows7 OS) and I am currently following the Costello methodology for data analysis for samples (n=11) which were sequenced last month using 454 pyrosequencing. I have managed to generate all of the correct files thus far in alpha diversity detection in the sample sequences. However, when trying to generate the separate rarefaction files using the rarefaction.single(freq=5) command in mothur, instead of generating 11 individual files ending with *.rarefaction mothur generates one file entitled SAMPLE.final.an.groups.rarefaction. Is this normal or should each sample analysed for its sequencing data have its own *.rarefaction file respectively? I have only just started using mothur last week so I am really a novice. If any forum users could offer me some much needed help with this I would greatly appreciate this.

Kind regards,

Paul.

2

The rarefaction.single command has a groupmode option, which defaults to true. If you want individual files for each sample, set groupmode=f.

3

Hi,

I appreciate the posibility to have all the groups in 1 output. Nonetheless I am interested in what order they are written to the table.
I am using R to plot the rarefaction curves and would like to add a legend and/or a color to each sample (MID) however in my ‘group’ column all groups have the same name:
_>data<-read.table(‘final.an.0.03.subsample.groups.rarefaction’,header=T)

head(data)
numsampled Group X0.03 lci hci
1 1 Bac_530f 1 1 1
2 1 Bac_530f 1 1 1
3 1 Bac_530f 1 1 1
4 1 Bac_530f 1 1 1
5 1 Bac_530f 1 1 1
6 1 Bac_530f 1 1 1_
I have 9 MID’s in total is there a way to know in what order they are in the final table?