adding taxonomy data to a feature-table.biom file

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1

Hi
I am using natively installed qiime2 on a Big Sur 11.3.1 macbook pro. I tried to use a script recommended on a previous post by @jairideout to add the taxonomy data to a feature-table.biom file using the following script:

biom add-metadata -i exported/feature-table.biom -o table-with-taxonomy.biom --observation-metadata-fp exported/biom-taxonomy.tsv --sc-separated taxonomy

feature-table.biom (74.6 KB)
biom-taxonomy.tsv (690.0 KB)

Here is the table-with-taxonomy.biom output file:
table-with-taxonomy.biom (142.0 KB)

Any help will be greatly appreciated.
Fernando

2

Hi @nietof,
I can not spot any obvious mistake in your command.
Could you please add the link to the post by @jairideout you mentioned above, as well as on what do you think went wrong and why, please?

Did you try to convert the the biom you created to a table to see what is in there with the following command:

biom convert -i table.biom -o table.from_biom_w_taxonomy.txt --to-tsv --header-key taxonomy

Cheers
Luca

3

Hi Luca
Here is the link to the post by @jairideout: Exporting and modifying BIOM tables (e.g. adding taxonomy annotations)

I figured out what was wrong. When I changed the header row in the biom-taxonomy.tsv file to show this column headers, #OTUID taxonomy confidence, I did it in excel and it didn't add the tab spacing. I repeated the editing using textedit with the tab spacing and now i can see the taxonomy column added to the feature table:

#OTU ID 1-1sum2020 1-1sum2021 1-3sum2020 1-3sum2021 1-4sum2020 1-4sum2021 1-5sum2020 1-5sum2021 1-7sum2020 1-7sum2021 2-1sum2020 2-1sum2021 2-3sum2020 2-3sum2021 2-4sum2020 2-4sum2021 2-6sum2020 2-6sum2021 2-7sum2020 2-7sum2021 3-1sum2020 3-1sum2021 3-2sum2020 3-2sum2021 3-3sum2020 3-3sum2021 3-4sum2020 3-4sum2021 3-6sum2020 3-6sum2021 4-1sum2020 4-1sum2021 4-2sum2020 4-2sum2021 4-3sum2020 4-3sum2021 4-4sum2020 4-4sum2021 4-5sum2020 4-5sum2021 taxonomy
6b315f08e0768a75fac2e33026b2bf5f 842.0 436.0 532.0 157.0 361.0 2930.0 742.0 773.0 307.0 1005.0 363.0 894.0 370.0 1041.0 380.0 1605.0 449.0 1248.0 1104.0 487.0 404.0 995.0 173.0 2192.0 1028.0 2274.0 1302.0 3506.0 2944.0 807.0 638.0 1472.0 589.0 552.0 925.0 1187.0 252.0 936.0 179.0 650.0 k__Bacteria; p__Acidobacteria; c__Acidobacteriia; o__Acidobacteriales; f__Koribacteraceae; g__; s__
a7886519b7bba11496199a24e256375a 535.0 696.0 215.0 354.0 361.0 278.0 763.0 617.0 458.0 1083.0 990.0 519.0 599.0 810.0 543.0 1285.0 576.0 1300.0 614.0 532.0 143.0 688.0 225.0 1446.0 521.0 965.0 190.0 680.0 314.0 925.0 356.0 677.0 263.0 651.0 357.0 678.0 1662.0 1123.0 194.0 1412.0 k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__; g__; s__
e19d2ae3bb9663795ab3089680a3f9cc 159.0 284.0 324.0 795.0 695.0 362.0 155.0 383.0 341.0 789.0 167.0 174.0 408.0 1197.0 259.0 426.0 382.0 790.0 329.0 341.0 135.0 91.0 120.0 519.0 647.0 520.0 190.0 2943.0 161.0 651.0 37.0 132.0 975.0 962.0 446.0 1089.0 344.0 498.0 321.0 1209.0 k__Bacteria; p__Acidobacteria; c__Acidobacteriia; o__Acidobacteriales; f__Koribacteraceae; g__; s__

Thank you so much for your help!!!
Regards
Fernando

1 Like
4

Hi,
well done and thank for letting us know so it coul dhelp other users!
Luca

5

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