hi
i am working with galaxy for analysis of metagenomics data. unfortunately i could not use the finch visualization.could you help me ,why pinch dont work for me
thank you
Dear @rez,
Can you please open up a new question, stating your error of the tool and describing more what you have tried to analyse. This post is not related to your question.
Thank you very much and have a nice day!
Florian
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Hi
I am analysis my metagenomics data by galaxy(https://metagenomics.usegalaxy.eu/) , everyathing is ok but when I want visualize data by fhinch as below
I could not make biom and system shows an answer like this:
I would appreciate if you help me to solve this problem.
Dear @rez,
Can you try to re-run the tool my assumption is that there was a hickup with Galaxy because of heavy traffic. However, if the error still comes up, then my next assumption is, that your data is either corrupted, empty, badly named or in the wrong format. So check first these things.
If you still struggle then you can share the history with me or here in the post (see Issue Reporting).
Have a good day and best wishes,
Florian
my history=reza nahai
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
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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:
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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.
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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?