Cluster tree calculated using Bray–Curtis dissimilarity, with jackknife values

[sdpapet]

Hi, I can't build a tree using Bray–Curtis dissimilarity, with jackknife values. Also, I can't make jackedknifed nMDS plots based on Bray–Curtis dissimilarity either.

I tried both methods using work flow script "jackknifed_beta_diversity.py" and step by step. For the workflow, I include the following specifies  changes in the parameter files

unweighted_unifrac,weighted_unifrac,bray_curtis
multiple_rarefactions_even_depth:num-reps 1000

However, the results don't give me any bray_curtis distance matrix. It still gives me the PCOA plot based on unweighted_unifrac and weighted_unifrac.

I have to used the 1000 subsample OTU tables in the rarefaction fold to do it by hand. Here are the problems.

1> I run beta_diversity.py using 1000 OTU tables as input fold and I get 1000 bray-curtis distance matrices.
2> I run upgma_cluster.py based on the matrices to build a UPGMA tree. I want to build one tree with node supporting information, but I get 1000 trees. I don't know how to build one tree with node supporting information ("master tree")
3> Similarly, I run "nmds.py" with the 1000 matrices. It will give me 1000 nmds coordinates files. I don't know how to combine them into a master file and plot it as the PCOA plot generated from "jackknifed_beta_diversity.py".
4> The last question. I am wondering if the PCOA plot generated from "jackknifed_beta_diversity.py" based on the average coordinates value of all iterations (1000 in this case).

[Luke Ursell]

Hi,

When you changed the parameter file, you need to make it look like:

beta_diversity:metrics unweighted_unifrac,weighted_unifrac,bray_curtis

The unifrac measurements are default, which is why they still appeared even though your parameter file wasn't quite right - see more here: http://qiime.org/documentation/qiime_parameters_files.html

I'd try the workflow script again with the updated parameter file.

Luke

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[Chiang Pet]

Hi Luke,

I think that's a typo. Sorry about that. I did exactly what you typed and the log file showed It ran three methods (unweighted_unifrac,weighted_unifrac,bray_curtis). I didn't get the bray_curtis matrices.

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[Luke Ursell]

Can you post your parameters file?

Luke

[sdpapet]

Hi Luke,

The attached files are my parameter file and the workflow log file. If you look at the log file, the workflow script can read my parameter file.

Ben

[Luke Ursell]

Hi Ben,

Try removing the .py from the first line of your parameters file so that it just reads:

beta_diversity:metrics bray_curtis,unweighted_unifrac,weighted_unifrac

Luke

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<jk_parameter.txt><log_20130705145747.txt>

[Chiang Pet]

Thank you, Luck. It worked after I fixed the parameter file.

Ben

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