Key outputs
Differentially modified output spreadsheet
Mako writes a TSV file of the following format:
differential/model_calls.tsv
transcript_id transcript_position rname chr chr_position estimate std_err test_statistic p_value model_type error error_message bh_corrected_p_value
ENST00000000233.10 145 ENST00000000233.10|ENSG00000004059.11|OTTHUMG00000023246.7|OTTHUMT00000059567.3|ARF5-201|ARF5|1032|protein_coding| chr7 127588556.0 0.28768207247673017 0.7936258469536126 0.3624908054356062 0.7169852932245568 binomial False 0.9640344056139295
ENST00000000233.10 178 ENST00000000233.10|ENSG00000004059.11|OTTHUMG00000023246.7|OTTHUMT00000059567.3|ARF5-201|ARF5|1032|protein_coding| chr7 127589106.0 0.1960495215844195 0.3689160678596121 0.531420392507882 0.5951274932453505 binomial False 0.9373782917763457
ENST00000000233.10 191 ENST00000000233.10|ENSG00000004059.11|OTTHUMG00000023246.7|OTTHUMT00000059567.3|ARF5-201|ARF5|1032|protein_coding| chr7 127589119.0 -0.7239188392266889 0.5913944974137653 -1.2240878844704635 0.220919075964312 binomial False 0.7249549006922915
ENST00000000233.10 195 ENST00000000233.10|ENSG00000004059.11|OTTHUMG00000023246.7|OTTHUMT00000059567.3|ARF5-201|ARF5|1032|protein_coding| chr7 127589123.0 0.49352123800261677 0.2511703485342725 1.9648865436649072 0.04942737051245885 binomial False 0.35089572319916346
ENST00000000233.10 229 ENST00000000233.10|ENSG00000004059.11|OTTHUMG00000023246.7|OTTHUMT00000059567.3|ARF5-201|ARF5|1032|protein_coding| chr7 127589157.0 -1.43281437674045 0.6961539005509063 -2.0581862367022326 0.039572259287345535 binomial False 0.307126201446428
...
Column |
Description |
|---|---|
transcript_id |
Transcript ID the site belongs to, extracted from rname |
transcript_position |
Transcript position of the site |
rname |
Full reference transcript annotation string |
chr |
Chromosome of the site |
chr_position |
Genomic position of the site |
estimate |
Effect size estimate from the differential model |
std_err |
Standard error of the estimate |
test_statistic |
Test statistic |
p_value |
Raw p-value for the test of differential modification at this site |
model_type |
Statistical model used to analyse the site (e.g. binomial, homo_norm, hetero_norm, beta_binomial) |
error |
Whether the model fit failed for this site (True/False) |
error_message |
Error message if error is True, otherwise typically blank/NA |
bh_corrected_p_value |
Benjamini–Hochberg corrected p-value |
Makoview launch script
Makoview is a visualisation tool to view the output of Mako.
It is automatically installed and can be launched using the script makoview/launch_makoview.sh.
All outputs
Directory tree of Mako outputs
outdir/
├── basecall
│ ├── <sample, e.g. H146>
│ │ ├── basecalled_sorted.bam
│ │ ├── basecalled_sorted.bam.bai
│ │ ├── H146_fastqc.html
│ │ ├── H146_fastqc.zip
│ │ ├── H146.flagstat.txt
│ │ └── 📁 nanoplot
│ ├── 📁 nanocomp
├── db
│ ├── coverage.duckdb
│ └── reads.duckdb
├── differential
│ ├── model_calls.tsv
│ ├── segments/*.parquet
│ ├── segments.csv
│ └── sites.duckdb
├── makoview
│ ├── launch_makoview.sh
│ └── 📁 makoview_venv
└── modcall
└── <sample, e.g. H146>
├── modifications_H146.tsv.gz
├── pileup_H146.bed.gz
└── pileup_H146.bed.gz.tbi
basecall/ directory
Per-sample basecalling and alignment QC.
| File | Description |
|---|---|
basecalled_sorted.bam(.bai) |
Coordinate-sorted, indexed alignments from dorado |
{sample}_fastqc.html/.zip |
FastQC report on basecalled reads |
{sample}.flagstat.txt |
samtools flagstat summary |
nanoplot/ |
Per-sample NanoPlot QC report |
nanocomp/ |
Cross-sample comparison (NanoComp) — read length, N50, throughput, identity, quality plots |
modcall/ directory
Per-sample RNA modification analyses (modkit).
| File | Description |
|---|---|
pileup_{sample}.bed.gz(.tbi) |
bedMethyl pileup of per-site modification stats |
modifications_{sample}.tsv.gz |
Read-level modification analyses |
db/ directory
Aggregated databases used internally by the differential step.
| File | Description |
|---|---|
reads.duckdb |
Read-level modification data across samples |
coverage.duckdb |
Per-site coverage across samples |
differential/ directory
Differential modification analysis outputs.
| File | Description |
|---|---|
model_calls.tsv |
Final differential analysis results |
sites.duckdb |
Selected/filtered sites used for testing |
segments.csv |
Genomic segments used to parallelise analysis |
segments/*.parquet |
Per-segment intermediate results |
makoview/
Interactive results viewer.
| File | Description |
|---|---|
launch_makoview.sh |
Script to launch the viewer |
makoview_venv/ |
Bundled Python virtual environment for the viewer |