analyzing several samples and techniques

Commands in mothur
1

Hi all,

I’m fairly new to microbiology and analyzing microbial community samples. I’ve been working through the example analyses for a couple of days now, and I can manage to process my pyrosequencing data.
However, I need to compare it to sequences obtained through cultivation.
How should I do this using mothur? How can I analyze the data both within and between samples AND techniques? Should I merge the data, and then just go through with ‘standard’ analysis?

I’ve been suggested to map the pyrosequences on the Sanger sequences, and get a table with presence/absence for both techniques per sequence, and then use this for ordination. Is this possible with mothur?

Something like this:

sequence pyrosequence cultivation
1        present      present
2        absent       present
etc.

Sorry for these very basic questions. If you know any good step-by-stap tutorials on how to start with this kind of analysis, please let me know. :oops:

Thanks in advance!

Sincerely

ps: I don’t know if this is the right section?

2

Hi Kirk,

Welcome to the wonderful world of microbial ecology :slight_smile: You would want to merge all your data into one table (we call them “shared files”) and then do your analysis. I’d suggest looking at the various analysis examples on the wiki (http://www.mothur.org/wiki/Analysis_examples). Although you aren’t likely to find an exact match for what you want to do, these examples will help you get a sense of how people analyze these types of data.

Also, be sure to sign up for the mailing list where we announce new releases and upcoming workshops (the next likely to be in December).

Pat

3

Thank you. It sure is challenging.

By standard analysis, I was referring to the examples, which indeed gave me a good insight into the procedures already. Anyway, when I get stuck, I’ll make some noise around this place.

Kind regards.