Question: About rarefaction curve : FROGS pipeline
gravatar for mailys.gauthier
21 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 • 635 views
ADD COMMENTlink modified 21 months ago by Jennifer Hillman Jackson24k • written 21 months ago by mailys.gauthier0
gravatar for Jennifer Hillman Jackson
21 months ago by
United States
Jennifer Hillman Jackson24k wrote:


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:

Best, Jen, Galaxy team

ADD COMMENTlink written 21 months ago by Jennifer Hillman Jackson24k


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

Best regards, Maïlys.

ADD REPLYlink written 21 months ago by mailys.gauthier0
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