I need some help regarding the taxonomic abundance.
i have got two datasets taxonomy and functional pathway abundance.
I want to known the relative abundance of a particular taxa in a particular function ( say relative abundance of proteobacteria in glycolysis pathway).
How can I do this,
@divyaprince321, It’s not clear to me what your data looks like, or what your goals are. If you can provide more information on what type of data you’re working with, what you’ve tried (or would like to try), and what your results might look like, that will probably make it easier for us to help.
Thanks I am done with it. However I need to work on something that I am confused with
I have got taxon id (1000148), but I need to decode it to particular taxa. I mean to say that what bacterial taxa is it. I am confused and not able to delineate these ids in ASVs file to particular taxonomy.
Please suggest me the exact commands how to run this.
Glad to hear it! You might consider sharing your approach here, so other users can benefit from your hard work.
Once again, more information would make this question easier to answer. Where did that taxon id come from? (Is it from a database? Is it something you created? What visualization or artifact data are you looking at, and what command did you run to produce it?)
I got created the biom table ( feature biom ) and it gave the ids now I want proper taxonomy.
for convenience I am attaching files feature-table.biom (2.0 MB)
It sounds like those are feature/ASV IDs, then, and not directly related to your taxonomy? How did you create the biom table?
An off-topic reply has been split into a new topic: The scikit-learn version used to generate this artifact does not match the current version of scikit-learn installed
Please keep replies on-topic in the future.
I am trying to known the contribution of each taxa towards a particular function.
For that I have done my analysis and I have got two files 1) the taxon id along with taxonomy and 2) the contribution of each taxa to function. Now the problem is that the taxon id are relatively larger in number and it is impossible to track each taxon id and its contribution manually. Now I want to know is there any particular command or script to do this.
thanks in advance
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