opening shared.file in excel - does not fully upload

Hello all,

I currently have an OTU table that was generated with the make.shared command, and it contains over 50,000 OTU’s. I would like to view this table in excel, however there are too many columns and as a result, it does not load all 50,000 OTU’s.

I am attempting to make a relative abundance chart in excel, however since it doesn’t fully upload I am unable. Is there a way to perhaps split the shared.file? Or is there another recommended program I can use to view the table? I am not used to this as I normally work with phylotype tables, and because those have much fewer columns those load just fine.

Thank you!

Well you can get relative abundance data out of mothur with the get.relabund command. What do you hope to get out of excel from a table with more than 50,000 columns? :slight_smile:

Well, typically I use the excel spreadsheet to sort my data from largest to smallest relative abundance, and its easy to build a chart from that. I don’t ever include all OTUs, only those above a certain number to compare the most abundant organisms from different samples/locations.

I wasn’t aware of the get.relabund command, I will try this.

Thank you!

One more question…is there a way to sort through the relabund file, so that I can grab/view the most abundant OTU’s? What I am trying to create is a bar plot where the most abundant OTUs per library can more easily be seen, however I am having trouble figuring out how to do this with the relabund file.

Thank you,

You’d probably have to write an R/Python script to pull out the relevant columns

Pat

Thank you, I wrote a quick script and it worked beautifully!