Transforming OTU data into sample counts

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 Gp1 0 1 0 0 0 0 0
6 Gp10 0 1 0 0 0 0 0
6 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 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.

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


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

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