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MMARINeDNA / metabarcoding_QAQC_pipeline

Pipeline scripts for initial quality control, ASV assignment, taxonomic classification, and preliminary data visualization
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Figure out the metadata! #4

Open avancise opened 1 year ago

avancise commented 1 year ago

We need to figure out a relatively painless way to get the metadata into the Miseq sequence file so that it can be pulled into phyloseq. This will also involve figuring out what we want our columns to be ahead of time and making all Miseq sequence files consistent downstream.

alexandriai168 commented 11 months ago

added a script called merge_metadata.R (the code is now also in the .qmd file) that has 2 inputs: -SampleSheetUsed.csv (the miseq sample sheet) -Hake_2019_metadata.csv (sample metadata sheet) it essentially sees what samples are present in the run (does some merging of names/data wrangling with the naming), and then merges in the sample metadata from Hake_2019_metadata.csv

let me know if that fixes this problem!