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Updated Practical 3 Processing 16S rRNA amplicon data (markdown) authored by Ben Francis's avatar Ben Francis
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Practical-3-Processing-16S-rRNA-amplicon-data.md
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...@@ -110,6 +110,7 @@ For now though, we're just going to use a (relatively) simple plotting function ...@@ -110,6 +110,7 @@ For now though, we're just going to use a (relatively) simple plotting function
We're all going to start today by making some plots. Sorry if the full dada processing took too long and you didn't get to run it all yourself. If you didn't, all you missed was running some R code and inspecting big unwieldy tables. We're all going to start today by making some plots. Sorry if the full dada processing took too long and you didn't get to run it all yourself. If you didn't, all you missed was running some R code and inspecting big unwieldy tables.
Start by getting the full processed dada data: Start by getting the full processed dada data:
# you don't need this if you created these objects yourself already
$ cp /bioinf/home/tfrancis/marmic2021/demultiplexed/seqtab_final.rds . $ cp /bioinf/home/tfrancis/marmic2021/demultiplexed/seqtab_final.rds .
$ cp /bioinf/home/tfrancis/marmic2021/demultiplexed/taxa_final.rds . $ cp /bioinf/home/tfrancis/marmic2021/demultiplexed/taxa_final.rds .
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