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(high-temp) No 7. Differentially Abundant ASVs & Taxa (16S rRNA/ITS) Output

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posted on 07.05.2022, 14:10 by Jarrod ScottJarrod Scott
Output files from the No 7. Differentially Abundant ASVs & Taxa Workflow page of the SWELTR high-temp study. In this workflow, we used the labdsv package to run Dufrene-Legendre Indicator Species Analysis and the microbiomeMarker package to run linear discriminant analysis (LDA) effect size (LEfSe) (Segata et al. 2011). We also used the microbiomeMarker package to assess the response of taxonomic lineages to soil warming.

da_wf.rdata: Contains all variables and objects (for 16s rRNA and ITS) from Differentially Abundant ASVs & Taxa analyses. To see the Objects, in R run load("da_wf.rdata", verbose=TRUE)

Additional files:

We also include all of the files (collected in zip archives) to reproduce the anvi'o figures from the paper, including profile databases, ASV dendrograms, sample dendrograms, additional layers data, additional views data, taxonomic profiles, etc.

If you have anvi'o installed, you can see an interactive verion of each figure from the paper by running the command:

anvi-interactive --view-data data.txt \
--tree asv.tre \
--additional-layers additional_layers.txt \
--profile-db profile.db \
--fasta-file ps_pime.fasta \
--manual


Please note, depending on when you access these data you may need to update the profile.db by running:

anvi-migrate profile.db --migrate-dbs-safely

ITS (its18_pime_anvio.zip)
16S rRNA (ssu_alpha_objects.zip)

Source code for the workflow can be found here:
https://github.com/sweltr/high-temp/blob/master/da.Rmd

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