Mirge3 Analysis

---
name: bio-small-rna-seq-mirge3-analysis
description: Quantifies known miRNAs, isomiRs, tRFs, and A-to-I editing fast with miRge3.0 by aligning collapsed reads to curated miRBase or MirGeneDB libraries. Use when choosing miRBase versus MirGeneDB as the reference; deciding whether to collapse isomiRs to the parent miRNA or keep 5'-isomiRs separate (they shift the seed and retarget); confirming the organism is among the six supported species; or remembering that RPM output is for display only and raw counts go to DESeq2/edgeR.
tool_type: python
primary_tool: miRge3
---

## Version Compatibility

Reference examples tested with: miRge3.0 0.1.4+, numpy 1.26+, pandas 2.2+

Before using code patterns, verify installed versions match. If versions differ:
- CLI: `miRge3.0 annotate --help` to confirm flag names (they have drifted across versions)
- Python: `pip show <package>` then `help(module.function)` to check signatures

If code throws ImportError, AttributeError, or TypeError, introspect the installed
package and adapt the example to match the actual API rather than retrying.

# miRge3 Analysis

**"Quantify my miRNAs and isomiRs fast"** -> Align collapsed reads to a hierarchy of curated small-RNA libraries and tabulate per-miRNA counts, isomiR variants, tRFs, and A-to-I editing.
- CLI: `miRge3.0 annotate -s sample.fastq.gz -lib LIBS -on human -db miRBase -a illumina -gff -ai -cpu 8 -o out/`

## The governing principle: miRge3 quantifies what is already known, fast, and isomiRs are biology

miRge3.0 does not do genome-wide de novo discovery as its main job; it Bowtie-aligns collapsed reads against small curated libraries (mature miRBase or MirGeneDB, hairpin, tRNA, rRNA, snoRNA, mRNA, spike-ins) hierarchically and assigns each read to the first matching class. That is why it is fast, and why it is the default for a routine differential-expression study on a supported species - and why it cannot help on an unsupported organism (it ships pre-built libraries for only six species: human, mouse, rat, zebrafish, nematode, fruitfly). For serious NOVEL discovery prefer miRDeep2; miRge3's optional `-nmir` SVM module is a convenience, not its strength.

Two judgments carry the analysis. First, isomiRs are real biology, not noise: a 5' isomiR shifts the seed (positions 2-7) and therefore the target set, so collapsing all isomiRs to the canonical miRNA can hide function - keep 5' isomiRs separate when isomiR identity is the question, and collapse to the parent only for a standard "which miRNAs changed" analysis. But the precision floor cuts the other way: low-count 3' and internal isomiRs are frequently sequencing/ligation artifacts (per-base error ~0.1-1% plus ligation bias), so filter them aggressively and demand replicate or UMI support, and trust 5' isomiRs more. A germline seed SNP (a polymiR) masquerades as an isomiR or edit; with genotypes available, fold them into the reference (e.g. OptimiR) rather than calling them isomiRs. Second, miRge3 emits both raw counts and RPM, but RPM is for display and cross-sample viewing only; differential testing takes RAW counts into DESeq2/edgeR, which model the count distribution themselves.

## Decision: miRBase vs MirGeneDB reference (`-db`)

| Reference | Size | Character | Choose when |
|-----------|------|-----------|-------------|
| miRBase (v22) | large (~1900 human miRNAs) | permissive; includes many dubious entries (mis-annotated tRFs/fragments) | maximizing recall / comparability with legacy studies |
| MirGeneDB | small (~550 human genes) | conservatively curated; every entry passes the biogenesis signature | conservative, high-confidence claims; cleaner DE feature set |

The reference choice changes results: counting against miRBase yields more "miRNA" rows, some of which are not bona fide miRNAs; against MirGeneDB the rows are fewer and defensible. miRge3 can emit both side by side - report which one a result came from, and pin the version.

## Library installation (no built-in download command)

```bash
# miRge3.0 has NO '--download-library' subcommand. Fetch the pre-built libraries from
# SourceForge and extract them, then point -lib at the extracted directory.
wget https://sourceforge.net/projects/mirge3/files/miRge3_Lib/human.tar.gz
tar -xzf human.tar.gz          # creates a 'human' library tree
# For an unsupported organism, build a custom library with the separate miRge3_build tool.
```

## Quantify known miRNAs (+ isomiRs, A-to-I)

**Goal:** Produce a per-miRNA count matrix with isomiR and editing detail for one or more samples.

**Approach:** Run `miRge3.0 annotate` with the curated library, organism, database, and adapter, switching on mirGFF3 isomiR output and A-to-I detection.

```bash
miRge3.0 annotate \
    -s sample1.fastq.gz,sample2.fastq.gz \
    -lib /path/to/miRge3_Lib \
    -on human \
    -db miRBase \
    -a illumina \
    -gff \
    -ai \
    -cpu 8 \
    -o output_dir

# -s: comma-separated FASTQs (raw or already adapter-known)
# -on: organism (human|mouse|rat|zebrafish|nematode|fruitfly)
# -db: miRBase or MirGeneDB
# -a: adapter as a name ('illumina') OR a raw sequence (e.g. TGGAATTCTCGGGTGCCAAGG)
# -gff: emit isomiR results in mirGFF3 (the community-standard isomiR format)
# -ai: A-to-I editing. A seed A->I edit RETARGETS the miRNA (inosine reads as G), and
#      mismatch-permissive alignment silently merges edited reads into the canonical
#      count - keep -ai on and treat seed edits as distinct species, not noise.
# -cpu: threads
```

## UMI and novel-miRNA options

```bash
# QIAseq UMI library: -qumi removes Qiagen PCR duplicates; -umi gives the 5',3' trim lengths
miRge3.0 annotate -s qiaseq.fastq.gz -lib LIBS -on human -db miRBase \
    -a AACTGTAGGCACCATCAAT -umi 0,12 -qumi -o out_umi

# Optional novel-miRNA prediction (SVM); needs the genome; prefer miRDeep2 for real discovery
miRge3.0 annotate -s sample.fastq.gz -lib LIBS -on human -db miRBase -a illumina -nmir -o out_novel
```

## Output files

| File | Description |
|------|-------------|
| miR.Counts.csv | Raw read counts per miRNA (this feeds DESeq2/edgeR) |
| miR.RPM.csv | RPM-normalized counts (display only, NOT for DE testing) |
| *.gff3 | isomiR variants in mirGFF3 (with `-gff`) |
| annotation.report.html / .csv | RNA-class composition and QC report |
| a2i / editing report | A-to-I editing sites and frequencies (with `-ai`) |

## Run from Python via subprocess

**Goal:** Orchestrate miRge3 from a Python pipeline and load its outputs.

**Approach:** miRge3.0 is a command-line tool with no documented Python API, so invoke it with subprocess, then read the CSV outputs with pandas.

```python
import subprocess

def run_mirge3(samples, lib_path, out_dir, organism='human', db='miRBase', adapter='illumina', threads=8):
    cmd = ['miRge3.0', 'annotate',
           '-s', ','.join(samples),
           '-lib', lib_path,
           '-on', organism,
           '-db', db,
           '-a', adapter,
           '-gff', '-ai',
           '-cpu', str(threads),
           '-o', out_dir]
    subprocess.run(cmd, check=True)
```

## Load and filter counts

**Goal:** Read the miRge3 count matrix and remove near-zero noise before downstream analysis.

**Approach:** Load `miR.Counts.csv`, then filter to miRNAs with a minimum total count (most miRBase entries are near-zero noise).

```python
import pandas as pd

def load_mirge3_counts(output_dir):
    return pd.read_csv(f'{output_dir}/miR.Counts.csv', index_col=0)

def filter_low_counts(counts, min_total=10):
    # Lower than an mRNA threshold because miRNA libraries have fewer total counts;
    # hand the SURVIVING RAW counts (not RPM) to DESeq2/edgeR for testing.
    return counts[counts.sum(axis=1) >= min_total]
```

## Aggregate isomiRs deliberately

**Goal:** Decide whether to collapse isomiRs to the parent miRNA or keep seed-shifting 5' variants separate.

**Approach:** Parse the mirGFF3 isomiR table, classify each variant by 5' vs 3' change, and aggregate to the parent only for variants that preserve the seed.

```python
def summarize_isomirs(isomir_counts):
    # 5' isomiRs shift the seed and retarget -> keep separate when isomiR identity is
    # the biology; 3' isomiRs mostly tune stability -> safe to collapse to the parent.
    # KEEP the -5p/-3p arm in the parent key: the two arms have different seeds and
    # targets and must never be merged (the dominant arm also switches across tissues).
    # .values assigns positionally - index.str.extract returns a fresh RangeIndex that
    # would otherwise misalign to all-NaN against the string index.
    isomir_counts['miRNA'] = isomir_counts.index.str.extract(r'(hsa-\w+-\d+[a-z]*(?:-[35]p)?)')[0].values
    summary = isomir_counts.groupby('miRNA').agg(
        total_reads=('count', 'sum'),
        n_isomirs=('count', 'count'),
        dominant_isomir=('count', lambda x: x.idxmax()))
    return summary
```

## Common Errors

| Symptom | Cause | Fix |
|---------|-------|-----|
| `unrecognized arguments: --isomir` | Flag does not exist | isomiR counts are produced by default; use `-gff` for mirGFF3 output |
| `unrecognized arguments: --download-library` | No such subcommand | Download libraries from SourceForge and `tar -xzf`; point `-lib` at the tree |
| `ModuleNotFoundError: mirge3.annotate` | No documented Python API | Call the CLI with `subprocess.run([...])` |
| Empty or tiny count matrix | Wrong `-on`, wrong `-db` case, or wrong adapter | Confirm a supported species; `-db miRBase`/`MirGeneDB`; check the adapter name/sequence |
| Organism not supported | Only six species ship libraries | Build a custom library with miRge3_build, or use miRDeep2/sRNAbench |
| Inflated DE significance on tiny miRNAs | RPM fed to the DE test | Feed RAW `miR.Counts.csv`, not `miR.RPM.csv`, to DESeq2/edgeR |

## Related Skills

- smrna-preprocessing - Adapter and UMI handling; miRge3 can also trim internally
- mirdeep2-analysis - Use when de novo novel-miRNA discovery is the goal
- differential-mirna - Differential expression from the raw count matrix
- trf-pirna-profiling - Deeper tRF/piRNA analysis beyond miRge3's tRF module

## References

- Patil AH, Halushka MK. 2021. miRge3.0: a comprehensive microRNA and tRF sequencing analysis pipeline. *NAR Genom Bioinform* 3:lqab068. doi:10.1093/nargab/lqab068
- Desvignes T, Loher P, Eilbeck K, et al. 2020. Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API. *Bioinformatics* 36:698-703. doi:10.1093/bioinformatics/btz675
- Kozomara A, Birgaoanu M, Griffiths-Jones S. 2019. miRBase: from microRNA sequences to function. *Nucleic Acids Res* 47:D155-D162. doi:10.1093/nar/gky1141
- Fromm B, Domanska D, Høye E, et al. 2020. MirGeneDB 2.0: the metazoan microRNA complement. *Nucleic Acids Res* 48:D1172-D1180. doi:10.1093/nar/gkz885
- Tan GC, Chan E, Molnar A, et al. 2014. 5' isomiR variation is of functional and evolutionary importance. *Nucleic Acids Res* 42:9424-9435. doi:10.1093/nar/gku656