yes, we used only the v4 region of the reference in the tutorial to speed up analysis, but you can use the full reference indeed
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hi.Dear
In order to analyze the metagenome, I have 3 samples, each of which contains 3 replications. I want to merge repetitions of each instance. How do I integrate the 3 repetition sequences for each sample ?In other words, now I have 9 sequence files, each with a forward file and a reverse file. Now I want to merge the iterations associated with each instance to finally analyze the three samples
.
hi.Dear
In order to analyze the metagenome, I have 3 samples, each of which contains 3 replications. I want to merge repetitions of each instance. How do I integrate the 3 repetition sequences for each sample ?In other words, now I have 9 sequence files, each with a forward file and a reverse file. Now I want to merge the iterations associated with each instance to finally analyze the three samples
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Hi @rez
Handling replicates has been asked/answered at the Mothur forum, please see: Search results for 'replicate' - mothur
i did it with galaxy. how can average every replication on one treatment?
Please avoid repeatedly asking the same question – especially not on other unrelated topics.
There isn’t a detailed Galaxy tutorial to cover your use case. But, the help at the Mothur website can be applied in Galaxy. The consensus is that you’ll have some choices about how to handle the replicates since Mothur was not originally designed to work with replicates. Example: assign all samples to distinct groups for some steps to compare within timepoints (quality control) and merge groups to compare across timepoints (explore differences).
Alternative tools may be a better choice. See the help, tools, and workflows at this domain-specific server for those examples: https://metagenomics.usegalaxy.eu/