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eolesin edited this page Apr 7, 2021 · 6 revisions

Working in QIIME2. Input is the "OTU table" that phyloFlash_compare.pl produces.

It does not need to go through rarefaction / relative abundance transformation. QIIME2 performs a normalization

on the data for beta diversity analyses.

Had a bit of trouble making sure the OTU table fit old qiime standards.

biom convert -i PhyloFlash_OTUformat1.csv -o species_otu_table.biom --table-type="OTU table" --process-obs-metadata taxonomy --to-json

qiime tools import --input-path species_otu_table.biom --type 'FeatureTable[Frequency]' --input-format BIOMV100Format --output-path feature-table-2.qza

In 2020 Dahle group sent 60 samples for sequencing from various chimneys across the AMOR. The wiki here is to share the pipeline I used to process this dataset. The intent is to be specific about all steps involved, and to provide other lab members with this information so that they do not have to repeat the same time-consuming processes. By using my Git page, there is an added benefit of accountability and having someone to email if something doesn't work for you. :)

Clone this wiki locally