Hi All,
I am looking for a specific OTU ( I have added the specific bacteria “species” I am looking for in the SILVA database)
It appears that those bacteria are in the low number OTUs (rare bacteria in the samples)…They are in Otu021126 and after…
I want to see in which samples you find them.
The problem is that excel doesn’t see more that 16000 columns for my .shared file
I am not sure to go around this?
Can anyone help?
Thanks!
kim
Can you use R?
library(dplyr)
otu <- read.table(file=YOURFILE.trim.contigs.good.unique.good.filter.precluster.pick.pick.an.unique_list.0.03.subsample.shared", header=T, stringsAsFactors = FALSE, row.names=2)
desired.otu <- select(otu, contains(“Otu021126”))
You can use the list.otulabels command, https://mothur.org/wiki/List.otulabels, to create an accnos file with the names of all the OTUs in your shared file. You can edit this file to include only the OTUs you are interested in looking at. Then you can use the get.otus command, https://mothur.org/wiki/Get.otus, to select those OTUs from your other files.
mothur > list.otulabels(shared=yourSharedFile)
mothur > get.otus(shared=yourSharedFile)
or
mothur > get.otus(list=yourListFile)
Great! thanks!! 