Transforming OTU data into sample counts

Commands in mothur
1

Hi everyone,

I have data that I processed through Mother using the MiSeq SOP. I have subsampled at 1000 sequencing reads and my OTU tax.summary file looks like this:

taxlevel rankID taxon daughterlevels total HRP-1 HRP-10 HRP-100 HRP-103 HRP-106
0 0 Root 1 10128 154 336 276 383 313
6 0.1.1.1.1.1.1 Gp1 0 1 0 0 0 0 0
6 0.1.1.2.1.1.1 Gp10 0 1 0 0 0 0 0
6 0.1.1.3.1.1.1 Gp11 0 1 0 0 0 0 1

I am being asked to make a relative abundance graph. Should I make this based upon this table? In the past I have used the wang.tax.summary file which gives the actual number of sequencing reads for each taxa. Is there a method to convert the OTU data so that I can know how many sequencing reads out of the 1000 that were clustered into each taxa listed? Thanks so much.

2

I’d do it with the shared file instead and use the cons.taxonomy file to find the labels for the column names.

Pat

3

Is there a command in Mothur that will replace the OTU columns with taxa identity from the taxonomy file?

4

what program are you using to generate the figures? If R, read in the taxonomy file along with the subsampled shared file, join the 2 on groups