Question: About rarefaction curve : FROGS pipeline
0
gravatar for mailys.gauthier
19 months ago by
mailys.gauthier0 wrote:

Hello everyone,

I am doing a metagenomic analysis on Galaxy with the pipeline FROGS. Everything works very well but I have a question for which I could'nt find the answer on the FAQs or anywhere... Briefly, I would like to compare my samples and, thereby, I would like to have the same number of sequences per sample. In the step "Affiliation stat", the software makes rarefaction curve. Does it calculates the minimum number of sequences for which the diversity is well represented for all the samples, and if so, where could I find this value? Does it use this number to subsampling the dataset for the abundance counts? Or do I have to subsample myself the dataset to have the same numbers of sequences per sample at the end of the analysis (and, if so, how could I subsample my sequences just before the affiliation step)?

Thank you in advance for your help, Maïlys.

galaxy • 557 views
ADD COMMENTlink modified 19 months ago by Jennifer Hillman Jackson23k • written 19 months ago by mailys.gauthier0
1
gravatar for Jennifer Hillman Jackson
19 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

Contacting the authors of this pipeline or a server that hosts the tools are probably the best source to get detailed methodology questions addressed.

Or, you may find some answers in here: http://bioinfo.genotoul.fr/index.php?id=165

Best, Jen, Galaxy team

ADD COMMENTlink written 19 months ago by Jennifer Hillman Jackson23k

Hello,

Thank you so much!! I found the answer on your link!

Best regards, Maïlys.

ADD REPLYlink written 19 months ago by mailys.gauthier0
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