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picrust / picrust2

Code, unit tests, and tutorials for running PICRUSt2
GNU General Public License v3.0
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determine the low depth samples #103

Closed ManarRashad closed 5 years ago

ManarRashad commented 5 years ago

Hi, I am new in using this tool and overall the bioinformatics field So could you help me to understand the number of observation in the output of: biom summarize-table -i table.biom and how I can determine through this output the low depth samples

Look forward to hearing from you Thanks

gavinmdouglas commented 5 years ago

Hey @ManarRashad,

biom is a dependency of PICRUSt2 and isn't written by me just so you know. You can read more about using the biom tools and summarizing table here.

The number of observations refers to the number of different features, whether they be operational taxonomic units, amplicon sequence variants, etc. These are the rows in a BIOM table and the samples are the columns.

You can see the depth per sample under Counts/sample detail:. What constitutes a low-depth sample can depend on the environment you're profiling. For instance, if there are only 3 taxa in the community then 100 reads would probably be sufficient, but for the human gut commonly at least 3000-4000 reads are required for each sample. There is no single cut-off accepted by the field however. You might also want to look at rarefaction curves to help determine the minimum depth requires for your environment of interest (see this tutorial).

Hopefully that helps!

Gavin

ManarRashad commented 5 years ago

Thanks a lot for clear explanation