songbird inquries

[Khalid_Ibrahim]

Hi Justine,
Thank you very much for comments foe for the longitudinal and paired sample comparisons with q2-longitudinal and it is helpful.
I am trying to run songbird but I have some inquiries in the bellow commands from the first step
What does mean "data/redsea/redsea.biom" or from where this file comes.

qiime tools import \
	--input-path data/redsea/redsea.biom \
	--output-path redsea.biom.qza \
	--type FeatureTable[Frequency]

Cheers

Khalid

[fedarko (Marcus Fedarko)]

The redsea.biom file there is an example "feature table" (stored in the BIOM format), containing abundance information for features (e.g. ASVs, OTUs) and samples.

Some QIIME 2 plugins will generate feature tables—for example, DADA2 or Deblur, if you run them through QIIME 2 (see the Moving Pictures tutorial for examples of this). In this case, these feature tables are saved as QZA files ("QIIME 2 artifacts")—these contain both the "table data" (e.g. a BIOM table file) and other internal information (for example, provenance data -- this enables us to look at a QZA file and see when it was created, how it was created, etc.). If you are interested, the QIIME 2 overview tutorial has a lot more information on QZAs.

However, often people might already have a BIOM table created from outside of QIIME 2 that they would like to use within QIIME 2. In this case, the command you posted above (qiime tools import ...) can be used to import a BIOM table file into QIIME 2, so that it can be used by a QIIME 2 plugin (like Songbird).

If you already have a feature table stored as a QZA file, and you want to run Songbird, you can just skip to the next command in the Songbird QIIME 2 tutorial (qiime songbird multinomial ...)