Top 20 Otu

Commands in mothur
1

Hi Mothur group,

I would like to know if there is any command in mothur to get top 50 OTU’s.
Its there for heatmap command but i think not in general for shared file.

Thank you in advance

2

You could use the split.abund command, http://www.mothur.org/wiki/Split.abund. Just set the cutoff to the size of the 50th OTU.

3

Thank you for reply!

Just to confirm i did following steps

  1. mothur “#deunique.seqs(fasta=Sample.subsample.fasta, name=Sample.subsample.names)”
  2. mothur “#split.abund(fasta=Sample.redundant.fasta,list=Sample.subsample.an.list,cutoff=50,group=Sample.subsample.groups)”
  3. mothur “#make.shared(list=Sample.subsample.an.unique.abund.list, group=Sample.subsample.unique.abund.groups, label=0.03)”

I did deunique before doing split.abund.

4

Almost, the cutoff should be the number of sequences in the 51th OTU. OTUs with abundances <= the cutoff are put into the “rare” file. Mothur sorts the OTUs by abundances, so if you look in the shared file at the OTU with the label 51 (OTU**51) and add up the abundances of all the groups, you will have the cutoff value. Here’s a simple example for top 4:


label Group numOtus Otu001 Otu002 Otu003 Otu004 Otu005... 0.03 F003D000 608 409 293 413 166 277 ... 0.03 F003D002 608 988 520 185 87 234 ... 0.03 F003D004 608 930 633 433 237 339 ... 0.03 F003D006 608 951 750 473 346 471 ... 0.03 F003D008 608 341 465 321 770 371 ... 0.03 F003D142 608 715 818 839 455 354 ... 0.03 F003D144 608 475 417 605 166 267 ... 0.03 F003D146 608 448 472 614 448 313 ... 0.03 F003D148 608 384 481 534 237 193 ... 0.03 F003D150 608 463 449 710 409 343 ...

OTU005 -> 277+234+339+471+371+354+267+313+193+343=3162

cutoff=3162 would give you the top 4 OTUs