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MetaPhlan3 -> Qiime rarefaction
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MetaPhlan3 -> Qiime rarefaction
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Qiime Taxonomic Analysis (after MetaPhlan3)
# Create Rarefaction Curves (All Kingdoms)
##--------------------------------
## Step 1: Summarize overall frequency feature table
## -------------------------------
### Summarize feature table
qiime feature-table summarize \
--i-table table.qza \
--o-visualization overall_summary
### Export summary
qiime tools export \
--input-path overall_summary.qzv \
--output-path overall_summary
## Determine --p-max-depth: look at "frequency per sample" and choose value around median or max frequency. Increase if needed (max freq per sample)
##--------------------------------
## Step 2: Create Rarefaction Plot
## -------------------------------
qiime diversity alpha-rarefaction \
--i-table table.qza \
--p-max-depth 57206464 \
--m-metadata-file sample-metadata.txt \
--o-visualization overall_alpha-rarefaction.qzv
##--------------------------------
## Step 3: Visualize rarefaction plot in qiime2 viewer
## -------------------------------
### View by shannon and observed features and by metadata
# Create Rarefaction Curves (Bacteria Only)
##--------------------------------
## Step 1: Summarize bacteria only table
## -------------------------------
### Summarize feature table
qiime feature-table summarize \
--i-table bacteria_only.qza \
--o-visualization bacteria_only_summary
### Export summary
qiime tools export \
--input-path bacteria_only_summary.qzv \
--output-path bacteria_only_summary
### Determine --p-max-depth: look at "frequency per sample" and choose value around median or max frequency. Increase if needed (max freq per sample)
##--------------------------------
## Step 2: Create Rarefaction Plot
## -------------------------------
qiime diversity alpha-rarefaction \
--i-table bacteria_species.qza \
--p-max-depth 1000000 \
--p-steps 5 \
--o-visualization bacteria_alpha-rarefaction.qzv
##--------------------------------
## Step 3: Visualize rarefaction plot in qiime2 viewer
## -------------------------------
### View by shannon and observed features and by metadata
# Create Rarefaction Curves (Eukaryota Only)
##--------------------------------
## Step 1: Summarize eukaryota frequency feature table
## -------------------------------
### Summarize feature table
qiime feature-table summarize \
--i-table eukaryota_only.qza \
--o-visualization eukaryota_only_summary
### Export summary
qiime tools export \
--input-path eukaryota_only_summary.qzv \
--output-path eukaryota_only_summary
### Determine --p-max-depth: look at "frequency per sample" and choose value around median or max frequency. Increase if needed (max freq per sample)
##--------------------------------
## Step 2: Create Rarefaction Plot
## -------------------------------
qiime diversity alpha-rarefaction \
--i-table eukaryota_only.qza \
--p-max-depth TBD \
--m-metadata-file sample-metadata.tsv \
--o-visualization eukaryota_alpha-rarefaction.qzv
##--------------------------------
## Step 3: Visualize rarefaction plot in qiime2 viewer
## -------------------------------
### View by shannon and observed features and by metadata
# Create Rarefaction Curves (Archaea Only)
##--------------------------------
## Step 1: Summarize arachaea frequency feature table
## -------------------------------
### Summarize feature table
qiime feature-table summarize \
--i-table archaea_only.qza \
--o-visualization archaea_only_summary
### Export summary
qiime tools export \
--input-path archaea_only_summary.qzv \
--output-path archaea_only_summary
### Determine --p-max-depth: look at "frequency per sample" and choose value around median or max frequency. Increase if needed (max freq per sample)
##--------------------------------
## Step 2: Create Rarefaction Plot
## -------------------------------
qiime diversity alpha-rarefaction \
--i-table archaea_only.qza \
--p-max-depth TBD \
--m-metadata-file sample-metadata.tsv \
--o-visualization archaea_alpha-rarefaction.qzv
##--------------------------------
## Step 3: Visualize rarefaction plot in qiime2 viewer
## -------------------------------
### View by shannon and observed features and by metadata
# Create Rarefaction Curves (Viruses Only)
##--------------------------------
## Step 1: Summarize viruses frequency feature table
## -------------------------------
### Summarize feature table
qiime feature-table summarize \
--i-table viruses_only.qza \
--o-visualization viruses_only_summary
### Export summary
qiime tools export \
--input-path viruses_only_summary.qzv \
--output-path viruses_only_summary
### Determine --p-max-depth look at "frequency per sample" and choose value around median or max frequency. Increase if needed (max freq per sample)
##--------------------------------
## Step 2: Create Rarefaction Plot
## -------------------------------
qiime diversity alpha-rarefaction \
--i-table viruses_only.qza \
--p-max-depth TBD \
--m-metadata-file sample-metadata.tsv \
--o-visualization viruses_alpha-rarefaction.qzv
##--------------------------------
## Step 3: Visualize rarefaction plot in qiime2 viewer
## -------------------------------
### View by shannon and observed features and by metadata