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borenstein-lab / burrito

A visualization tool for exploratory data analysis of metagenomic data
https://elbo-spice.gs.washington.edu/shiny/burrito/
GNU General Public License v3.0
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error working with picrust2 outputs in burrito #27

Open marwa38 opened 2 years ago

marwa38 commented 2 years ago

Hello .. could you please help me why I am getting this error (screenshot attached below)?

I used three files (attached in .zip; all in .tsv) 1- ASVs count table (I don't have an OTU table, not sure if that is a problem?) added in taxonomic abundance option 2- ASV_taxonomy added in taxonomy: custom taxonomy (I aligned against silva) 3- pred_metagenome_unstrat added in Taxonomy-function linking method: Function Attribution table option burrito.zip

other options were left as default

image

your help is very much appreciated. Marwa

engal commented 2 years ago

Hi Marwa,

Using ASVs is fine, there shouldn't be a problem there. The pred_metagenome_unstrat table you're providing is a function abundance table, not a function attribution table. PICRUSt2's stratified option combined with PICRUSt2's convert_table.py script will produce a function attribution table that you can use as input for BURRITO's function attribution option (see here for more details).

Hope that helps!

marwa38 commented 2 years ago

thanks that is helpful @engal
regarding issue #21; is it possible to use KO_predicted as inputs, currently?

marwa38 commented 2 years ago

I tried adding pred_metagenome_contrib.legacy.tsv instead but in all of my trails the server disconnected on its own not sure why, any advice please or guidance?

engal commented 2 years ago

You should be able to use the KO_predicted file as input for the genomic content option.

If you are having connection issues with the server, you can try testing it with a smaller version of your dataset to make sure that you are able to upload files to the server. You can also make sure that you are on a wired connection, and you can also test on a different network to see if it's an issue with the network you are on.