Dear flow
i would appreciate if you tell me what is the means of more in bellow chart?
i think there is not either corrupted, empty, badly named or in the wrong format because I still have the same problem when I use my own Galaxy data below.
Dear @rez,
I deleted one of the previous post for you for your own safety. Please look at the link I have provided and also this one Galaxy 101. To know how to share a history.
The more means that there are more taxa, but because of the current zoom level you cannot see it. It should zoom in, if you double click on the region.
Cheers,
Florian
1 Like
Thank you for answering me patiently.
I used Galaxy data to analyze the data
but I still can’t create make biome and I can’t see the results in Finch.
Hi! Could you check for me the sample names in the collection you made right after the upload step? Errors can happen in make.biom step if the sample names in your history don’t match those in the metadata file. Your collection should look something like this:
Oh, actually your error message looks a bit different. Could you share your history with me (via link)? Here is instructions how you can do that: Sharing your History
Then I can see if I can see what is going wrong for you.
on the hand i want know about percentages of bacteria in samples but i dont know
> Hands-on:
MetaPhlAn2
please send me hands on of MetaPhlAn2 to get percentages of bacteria in samples of metagenome data
Thanks for sharing your history. I see that you are using your own datasets here, not the tutorial data. This means you will also have to create your own metadata file (e.g. if you have groups). You can also create the biom file without such a metadata file as a start. I was able to create this biom file and view it in Phinch.
Also to answer your earlier questions about the "16 more… " in the Krona plot: this means there are a lot more taxons at that level that could not be displayed in this view, but you can click on taxons to “zoom in” in Krona to see what these additional entries are. For example:
1 Like
how can i create your own metadata file? and how can i can also create the biom file without such a metadata file as a start?
on the hand i want know about percentages of bacteria in samples but i dont know
> Hands-on:
MetaPhlAn2
please send me hands on of MetaPhlAn2 to get percentages of bacteria in samples of metagenome data
Have a look at the metadata file from the tutorial. It is a pretty simple 2-column format of
sample name - metadata value
This metadata can be whatever makes sense for your data. In the tutorial we cared about the age of the mouse, so column 2 was the age of the mouse in days. For your experiment that might be something else (or nothing). For the make.biom step, the metadata file is an optional input, so just repeat the step but don’t provide any metadata file, and then view it in Phinch.
I am not sure about your question about MetaPhlan2, this tutorial is for 16S data and also provides percentages of bacteria (e.g. in the krona plot). There are other tutorials in the Metagenomics section of the GTN that cover whole-genome shotgun datasets that use MetaPhlaN, so you can have a look at those too.
1 Like
In the tutorial section in order to analyze the data from the area V4 used from * `silva.v4.fasta as
reference - Reference to align with
` but my data primer extention V1 v3 region of the 16S gene. so can i will use from silva gold for allign or not?
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
1 Like
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
1 Like
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/