How to get dominant OTUs?

Commands in mothur
1

Hi,
I am not sure if there is any topic about this. My question would be stupid as i am a beginner with mothur

I am done with my analysis, and now I can sort up to know which OTUs are dominant in my samples. However, i would like to get the sequences of these dominant OTUs in order to classify them in species level. Could any one can tell me if mothur has any command for this purpose?

I can do manually but it seems to be time consuming as i have many samples. I guess there should be the command allowing me to pull out these OTUs with sequences.

Thanks in advance,

2

hi

I am also a beginner with mothur.I think you can try to run the command " get.oturep", then you can obtain the fasta-formatted sequence file containing only a representative sequence for each OTU.

you can visit the webset: http://www.mothur.org/wiki/Get.oturep. I hope this can help you !

best whish!

3

Thanks,

I actually tried with that, and it said that in version 1.31.0, the method parameter was added in order to get the most abundance sequences in OTU cluster
(to refer to this topic get.oturep - most abundant as representative)

However, there is no clear guilline for the command structure. Should it be like
mothur > get.oturep(column=96_lt_column_amazon.dist, name=amazon.names, fasta=amazon.fasta, list=98_sq_phylip_amazon.fn.list, group=amazon.groups, method=abundance/most abundance/distance???)

Please help me out if anyone have been practicing with this!

Thanks

4

Sorry, i think i got it. The command is
mothur > get.oturep(column=96_lt_column_amazon.dist, name=amazon.names, fasta=amazon.fasta, list=98_sq_phylip_amazon.fn.list, group=amazon.groups, method=abundance)