subsampling when only working with one phyla

Theory behind mothur
1

When I run get.lineage there is no slop OTU that’s keeping track of the total sequences for each sample. Is this intentional? Is there a theoretical community ecology reason that we shouldn’t subsample a particular phyla using the numbers from the whole community? I can add it back in, but wanted to know why it isn’t there (similar to the slop OTU in split.abund)

2

When I run get.lineage there is no slop OTU that’s keeping track of the total sequences for each sample. Is this intentional?

The get.lineage and remove.lineage commands were designed to select sequences that classified to a set of taxonomies you are interested in or to remove contaminants from your dataset usually on fasta and associated files. With the addition of the constaxonomy parameter, a “removed” or “unselected” OTU option could be added. Is this a feature request that would be helpful for you?

Is there a theoretical community ecology reason that we shouldn’t subsample a particular phyla using the numbers from the whole community? I can add it back in, but wanted to know why it isn’t there (similar to the slop OTU in split.abund)

We don’t include these sequences in the subsample because they are part of the screening process. We want to reduce sequencing errors as much as possible by the steps outlined in Pat’s example analysis’, http://www.mothur.org/wiki/454_SOP and http://www.mothur.org/wiki/MiSeq_SOP, including the removal contaminates and chimeras.

Kindly,
Sarah

3

Hi Sarah

I think it would be useful to have the “removed OTUs” for the way that I’m using get.lineage. I like to think about this in the insect pit trap way-I’m capturing most of the bacterial community with my sequencing “pit trap” even if for some analyses I’m only interested in a particular group-say dung beetles. But it’s difficult to compare two pit trapped samples of dung beetles unless I know how many other insects I caught. Does one trap have 3 dung beetles rather than 100 because it just wasn’t in as good a location? or were there way more stink bugs in that location than there were in the dung beetle heavy location?

thanks Kendra*

*clearly not actually an entomologist