Tax4fun output visualization

[selin-kucukavsar]

Hello,

I have used tax4fun to predicts the functional capabilities of my microbial communities on 16S data samples. It gives a output file as . txt and below how it looks like:

Can I use Krona to visualize these data ? I have no idea how to convert the tax4fun output file that can be readable by krona.

Thanks, any help is appreciated, Selin

[ashishdamania]

See this link: https://github.com/marbl/Krona/wiki/Importing%20text%20and%20XML%20data If you have a "Quantitative" field in the first column for example: http://krona.sourceforge.net/examples/text.txt you should be able to use ./ImportText.pl script to import the data. Also, you can use -q option in script if there is no quantity/numerical field. In your case, not sure what the last column represents. Is it e-value or something similar?

[selin-kucukavsar]

Thanks for the answer, i will give it a try. Last column should be something like abundance, i am not really sure :)

I have problem with the script updateAccessions.sh. I had no problem with the ./install.pl and ./updateTaxonomy.sh. I am using OSX: 10.12.3

After I run the code I have the following:

_**> mac-sinan:KronaTools-2.7 selinkucukavsar$ ./updateAccessions.sh Fetching accession2taxid/dead_nucl.accession2taxid.gz... Fetching checksum... Checksum for accession2taxid/dead_nucl.accession2taxid.gz matches server. Fetching accession2taxid/dead_prot.accession2taxid.gz...

Update failed. Is your internet connection okay?**_

My connection has no problem. I am the owner of the computer but I am installing it to my home directory. Can that be problem? Or is it possible using without the update.

If you could help any further, that would be great. Selin

[ashishdamania]

I guess you will be fine running just updateTaxonomy.sh. No need to run updateAccessions.sh. I think you will be fine without running any taxonomy scripts if you only need to visualize Kegg pathway results. First, you need to find what the last column in your data represents. It is just the matter of switching the columns and importing the data into Krona using ./ImportText.pl.

[selin-kucukavsar]

Thanks a lot for the. I will post what is the last column is in case someone else will need it. Selin

On 13 Apr 2017 17:18, "deepthoughts" [email protected] wrote:

I guess you will be fine running just updateTaxonomy.sh. No need to run updateAccessions.sh. I think you will be fine without running any taxonomy scripts if you only need to visualize Kegg pathway results. First, you need to find what the last column in your data represents. It is just the matter of switching the columns and importing the data into Krona using ./ImportText.pl.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/marbl/Krona/issues/47#issuecomment-293908768, or mute the thread https://github.com/notifications/unsubscribe-auth/AaJ8w8lg1jyw9Vgg4JwGp9pxILrbVPbyks5rvi7BgaJpZM4M8rYz .

[ondovb]

Hi @selin-kucukavsar, It looks like that first column is KEGG ortholog identifiers with their leaf names. In order to use ktImportText as @deepthoughts recommends, you would need to somehow expand those to their full lineages (e.g. starting from "Metabolism," then to "Carbohydrate metabolism" on down). Also note that KEGG is not officially supported by Krona because its ontology is a directed acyclic graph rather than a tree, i.e. a KEGG ortholog can belong to multiple parents, which is just something to bear in mind while viewing the chart. Another option would be to translate the KEGG IDs to Enzyme Commission numbers, which are strictly hierarchical and can be imported into Krona directly with ktImportEC.

[emankhalaf]

Hello, I have a similar problem, I posted it as a new issue yesterday, but did not get any answer. I would like to use krona to display Tax4Fun output: 0.008833584 Metabolism carbohydrate metabolism Glycolysis / Gluconeogenesis 0.006236372 Metabolism carbohydrate metabolism Citrate cycle (TCA cycle) 0.008593556 Metabolism carbohydrate metabolism Pentose phosphate pathway 0.005395773 Metabolism carbohydrate metabolism Pentose and glucuronate interconversions

I installed Krona as following: curl -LOk https://github.com/marbl/Krona/releases/download/v2.7/KronaTools-2.7.tar sudo ./install.pl sudo ./updateTaxonomy.sh sudo ./updateAccessions.sh

However, I am going to use krona with only regular data stored in text files (as above) not taxonomy files. I am just following the tutorial

I copied the files in kronaTools-2.7 folder and then use this command: ktImportText control.text -o ctrl_krona.html I got this error: No such file or directory at /usr/local/bin/ktImportText line 71. I tried this command; module load kronaTools and got this error; module: command not found (I don't know the correct order for using krona) Then tried: KtImportText control.txt -o control.html

got this: KtImportText: command not found

How to load/activate krona before using the arguments??

Thanks

[Sharma2019]

Hello! Do you guys know what these numbers mean in the Tax4Fun output?

[ashishdamania]

Looking at the files downloaded from the Tax4Fun website http://tax4fun.gobics.de/ , it seems that the file "Tax4Fun.Rd" has the explanation of the output from the Tax4Fun function.

A list containing the predicted functional or metabolic profiles and the FTU statistics Tax4Fun.Rd.txt

Or it might be just the p-value. Refer to the bibliography on this page. http://tax4fun.gobics.de/#foot9

This is the closest I can find anything on those numbers.

Thanks!