Question: Microbiome data: Should unmatched reads be included in Shannon Diversity calculations?
0
gravatar for Lina F
3.2 years ago by
Lina F150
Boston, MA
Lina F150 wrote:

Hi all,

I was wondering how everyone deals with unmatched reads when calculating Shannon Diversity.

Since they may be valid sequences and match an unknown 16S sequence, should they be included?

Or is it skewing the analysis because they most likely don't all come from the same organism?
In that case, is it safe to just discard them?

Thanks for any thoughts!
~Lina

ADD COMMENTlink written 3.2 years ago by Lina F150

Normally, I would expect the researcher to cluster reads, and determine whether a sequence is valid based on cluster size and purity regardless of whether the sequence matches anything known.

ADD REPLYlink written 3.2 years ago by Brian Bushnell16k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1386 users visited in the last hour