AMaNITA Report
07 July, 2025
Summary
Settings
Metadata Table
Filter Details
Reference Assumptions
Generated Plots
Filtering Module
Plots generated by the filtering module can be found at: /users/enovoa/fpelizzari/amanita_projects/laia_yeast_trnas/all/ftbp/filtering/plots
Technical Module
Plots generated by the technical module (pre-filtering) can be found at: /users/enovoa/fpelizzari/amanita_projects/laia_yeast_trnas/all/ftbp/technical_{pre or post}/plots
Batch Module
Plots generated by the batch module can be found at: /users/enovoa/fpelizzari/amanita_projects/laia_yeast_trnas/all/ftbp/batch/{comp_variable}/plots
Pairwise Module
Plots generated by the pairwise module can be found at: /users/enovoa/fpelizzari/amanita_projects/laia_yeast_trnas/all/ftbp/pairwise/{comp_variable}/{comp_ID}/plots
Report
Plots generated for the report can be found at: /users/enovoa/fpelizzari/amanita_projects/laia_yeast_trnas/all/ftbp/report/plots
Input abundance and modification data tables can be found at: /users/enovoa/fpelizzari/amanita_projects/laia_yeast_trnas/all/ftbp/report
Quality Control Metrics
Input Abundance Data
Table
Replicability Scatterplots
Correlation Plot
png 2 png 2Exploratory PCAs
Abundance
comp_OX_STRESS
batch_RunID
Modifications
comp_OX_STRESS
batch_RunID
Filtered Reads
Table
Number of Reads filtered
Normalized Number of Reads filtered
Percentage of Reads filtered
tRNA Isoacceptor fraction
Pre-filtering
Post-filtering
tRNA Gene fraction
Pre-filtering
Post-filtering
tRNA Gene fraction, norm per Isoacceptor
Pre-filtering
Post-filtering
Read Composition per Sample
Pre-filtering
Post-filtering
Read Composition per tRNA Gene
Pre-filtering
Post-filtering
Full-length fraction
Pre-filtering
Post-filtering
3’ Reads fraction
Pre-filtering
Post-filtering
5’ Reads fraction
Pre-filtering
Subset Reads fraction
Pre-filtering
Ligation Efficiency Score
Pre-filtering
Post-filtering
Degradation Score
Pre-filtering
Post-filtering
Batch Effect Investigation
comp_OX_STRESS
Principal Variance Component Analysis
PVCA Plot for Potential Batch Effects
PVCA Plot for All Effects
PVCA error: Error: number of levels of each grouping factor must be < number of observations (problems: comp_OX_STRESS:batch_RunID)
Batch Variables to Adjust for
Suggested models
Accounting for Batch Effects
Batch Effect-Corrected PCA Plots - Abundance
model_1
Batch Effect-Corrected PCA Plots - Modifications
model_1
CONTROL vs YES
Below are the results for the comparison: comp_OX_STRESS.CONTROL_vs_YES