different results by shhh.flows command

Commands in mothur
1

I run the shhh.flows command with the same parametes several times, but got a little different results each time.

I did’t understand the theory of this command and I’m not sure if the different results are reasonable.

Looking forward to your reply.

Thanks!

2

It’s reasonable, but the differences shouldn’t be huge. There is a clustering step to get going and there is some randomness there.

3

Thanks pschloss!
Moreover, are you familiar with the theory of this command and can you tell me more about it?

4

For most of the commands if you run the command with the citation option you’ll find a list of papers you can get on the command…

mothur > shhh.flows(citation)

Schloss PD, Gevers D, Westcott SL (2011).  Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies.  PLoS ONE.  6:e27310.
Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ (2011).  Removing noise from pyrosequenced amplicons.  BMC Bioinformatics  12:38.
Quince C, Lanzén A, Curtis TP, Davenport RJ, Hall N, Head IM, Read LF, Sloan WT (2009).  Accurate determination of microbial diversity from 454 pyrosequencing data.  Nat. Methods 6:639.
http://www.mothur.org/wiki/Shhh.flows
5

I appreciate your help very much. :slight_smile:

6

Hi, I have the similar problem ,the flow was 1779.According to the 454SOP, i should use the trim.seq(Using quality scores).but the result was not well, scrap was too much. I know you use the trim.flows.can you tell me the command lines,the minflows=?maxflows=?

7

You have to use flows=B for trim.flows and shhh.flows. Do you know which image processing pipeline your sequence provider used? If it was one of the long amplcons you can probably safely use 1000 flows