TonyaWard
commented
4 years ago Hi Sandipan,
Can you please share the files?
Thanks!
From: Sandipan Samaddar notifications@github.com Sent: Wednesday, July 8, 2020 2:56 PM To: knights-lab/BugBase BugBase@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [knights-lab/BugBase] Bugbase says incorrect biom file format (#13)
Hi, I used dada2 for analyzing the 16S dataset and now I am trying to predict high-level phenotypes in the data using Bugbase. But while outputting the biom file I am facing some problems. I am not sure what is going wrong but any help will be appreciated.
Bugbase documentation says it needs a OTU table in BIOM format (version 1.0, JSON) picked against a GG database. (https://bugbase.cs.umn.edu/documentation.html)
I used GG database to classify sequences and created a biom file which looks fine to me but its not working and it says not a correct format.
The commands used to generate the biom file were :
In R using biomformat package:
biom16S <- make_biom(count_tab16s ) biom_file <- biom16S outfile = tempfile() write_biom(biom_file, outfile)
where count_tab16S is the count file with ASV IDS in rows and sample names in columns.
After getting the output I added the metadata in terminal using the command:
biom add-metadata -i my.biom -o table-with-taxonomy.biom --observation-metadata-fp taxonomyfile.tsv --sc-separated Taxonomy
where taxonomyfile.tsv is the file with GG taxonomy information.
After getting the output from the above step I converted the file to JSON:
biom convert --table-type="OTU table" -i table-with-taxonomy.biom -o your_OTU_table.txt --to-tsv --header-key taxonomy biom convert -i your_OTU_table.txt -o OTU_table.biom --table-type="OTU table" --to-json --process-obs-metadata taxonomy
I used the output in Bugbase but it didnt work.
But when I validated the file using: biom validate-table -i OTU_table.biom
it says its a correctly formatted file.
On the other hand, I also used Mothur to process my sequences and created biom file using make.biom command and converted file to json the same way I did above but it worked with Bugbase.
So I am afraid whats going wrong.
I will also be happy so share any files if needed.
Thanks,
Sandipan
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sandipansamaddar
Hi, I used dada2 for analyzing the 16S dataset and now I am trying to predict high-level phenotypes in the data using Bugbase. But while outputting the biom file I am facing some problems. I am not sure what is going wrong but any help will be appreciated.
Bugbase documentation says it needs a OTU table in BIOM format (version 1.0, JSON) picked against a GG database. (https://bugbase.cs.umn.edu/documentation.html)
I used GG database to classify sequences and created a biom file which looks fine to me but its not working and it says not a correct format.
The commands used to generate the biom file were :
In R using biomformat package:
where count_tab16S is the count file with ASV IDS in rows and sample names in columns.
After getting the output I added the metadata in terminal using the command:
biom add-metadata -i my.biom -o table-with-taxonomy.biom --observation-metadata-fp taxonomyfile.tsv --sc-separated Taxonomywhere taxonomyfile.tsv is the file with GG taxonomy information.
After getting the output from the above step I converted the file to JSON:
I used the output in Bugbase but it didnt work.
But when I validated the file using:
biom validate-table -i OTU_table.biomit says its a correctly formatted file.
On the other hand, I also used Mothur to process my sequences and created biom file using make.biom command and converted file to json the same way I did above but it worked with Bugbase.
So I am afraid whats going wrong.
I will also be happy so share any files if needed.
Thanks,
Sandipan