Diversity analysis with OTU table text file

moving-pictures
silva
otus
diversity

(Chris) #1

Hello - complete newbie here. Trying to generate alpha and beta diversity core metrics from my data that I received today. I want to apply the command: qiime diversity core-metrics-phylogenetic
however I am not sure how to generate the requisite qza files needed as inputs

What I have is a OTU table (.txt) formatted as such:
OTU ID sample… sample… sample… … sample_

a metadata file formatted as a .tsv that looks like the one from the tutorial
and a fasta file (unaligned) (.fa)

Sequences were processes with dada2 v 1.8 and bacterial taxonomy was assigned from the Silva training set silva_nr_v132_train_set.fa.gz. Data is unfiltered.

From my understanding, this dataset is ready to proceed with steps outlined in https://docs.qiime2.org/2018.11/tutorials/overview/#diversity-analysis. However, I am not able to generate the artifact files necessary to move forward (table.qza) as I do no have EMPSingleEndSequences sorted taxa.

Any idea how I would proceed? Or is it not possible with what I have been given?

Thanks for any help!


(Justine) #2

Hi @firefoxmicrobiom,

Welcome!

I’d suggest converting your data to biom, using the command, biom convert. This is outside of QIIME, but will get the data properly formatted. So, for instance, if my table is otu_table.txt, then I would run the comamnd,

biom convert \
 --i-input-file ./otu_table.txt \
 --o-output-pfile ./otu_table.biom \
 --to-hdf5 \
 --table-type otu_table

If you have taxonomy, you may want to specify that with the --process-obs-metadata flag.

And then checking out the Data Import tutorial, specifically the section talking about feature tables.

If your unaligned fasta file is your deprelicated sequences, you’re in a good place to build a tree. (Which I would highly recommend.) The data import tutorial also addresses importing the sequences.

Best of luck and happy QIIME-ING :qiime2:!

Best,
Justine


(Chris) #3

I think that could work. Thanks!


(system) #4

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