AMaNITA Report
08 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//plasmodium_asexual/all/ftbpc/filtering/plots
Technical Module
Plots generated by the technical module (pre-filtering) can be found at: /users/enovoa/fpelizzari/amanita_projects//plasmodium_asexual/all/ftbpc/technical_{pre or post}/plots
Batch Module
Plots generated by the batch module can be found at: /users/enovoa/fpelizzari/amanita_projects//plasmodium_asexual/all/ftbpc/batch/{comp_variable}/plots
Pairwise Module
Plots generated by the pairwise module can be found at: /users/enovoa/fpelizzari/amanita_projects//plasmodium_asexual/all/ftbpc/pairwise/{comp_variable}/{comp_ID}/plots
Pairwise Custom Module
Plots generated by the pairwise-custom module can be found at: /users/enovoa/fpelizzari/amanita_projects//plasmodium_asexual/all/ftbpc/pairwise/{comp_variable}/{comp_ID}/plots, similarly to the pairwise module
Report
Plots generated for the report can be found at: /users/enovoa/fpelizzari/amanita_projects//plasmodium_asexual/all/ftbpc/report/plots
Input abundance and modification data tables can be found at: /users/enovoa/fpelizzari/amanita_projects//plasmodium_asexual/all/ftbpc/report
Quality Control Metrics
Input Abundance Data
Table
Replicability Scatterplots
Correlation Plot
png 2 png 2Exploratory PCAs
Abundance
comp_Stage
comp_RTvsS
batch_RunID
Modifications
comp_Stage
comp_RTvsS
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_Stage
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_Stage:batch_RunID)
Suggested models
No batch effects detected
comp_RTvsS
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_Stage:batch_RunID)
Suggested models
No batch effects detected
R vs S
Below are the results for the comparison: comp_Stage.R_vs_S
Differential Abundance
Examined models
Default
Custom
DESeq2 Results Table
model_0
custom_3
Volcano plots
model_0
custom_3
Heatmaps
model_0
custom_3
Differential Modifications
edgeR Results Table
model_0
custom_3
Volcano plots
model_0
custom_3
Positional Heatmaps
model_0
custom_3
Positional Barplots
model_0
custom_3
R vs T
Below are the results for the comparison: comp_Stage.R_vs_T
Differential Abundance
Examined models
Default
Custom
DESeq2 Results Table
model_0
custom_1
Volcano plots
model_0
custom_1
Heatmaps
model_0
custom_1
Differential Modifications
edgeR Results Table
model_0
custom_1
Volcano plots
model_0
custom_1
Positional Heatmaps
model_0
custom_1
Positional Barplots
model_0
custom_1
S vs T
Below are the results for the comparison: comp_Stage.S_vs_T
Differential Abundance
Examined models
DESeq2 Results Table
model_0
Volcano plots
model_0
Heatmaps
model_0
Differential Modifications
edgeR Results Table
model_0
Volcano plots
model_0
Positional Heatmaps
model_0
Positional Barplots
model_0
RT vs S
Below are the results for the comparison: comp_RTvsS.RT_vs_S
Differential Abundance
Examined models
Default
Custom
DESeq2 Results Table
model_0
custom_4
Volcano plots
model_0
custom_4
Heatmaps
model_0
custom_4
Differential Modifications
edgeR Results Table
model_0
custom_4
Volcano plots
model_0
custom_4
Positional Heatmaps
model_0
custom_4
Positional Barplots
model_0
custom_4
T vs S
Below are the results for the comparison: comp_Stage.T_vs_S