Output#

MirMachine writes intermediate files under data/ and analyses/ and final run outputs under results/predictions/.

Main Output Layout#

For --species ExampleSpecies, the key files are:

data/yamls/ExampleSpecies.yaml
results/predictions/gff/ExampleSpecies.PRE.gff
results/predictions/filtered_gff/ExampleSpecies.PRE.gff
results/predictions/fasta/ExampleSpecies.PRE.fasta
results/predictions/heatmap/ExampleSpecies.heatmap.csv

Interpretation#

results/predictions/gff/*.PRE.gff: Unfiltered predictions after overlap resolution.
results/predictions/filtered_gff/*.PRE.gff: High-confidence subset after family-specific trusted cutoff filtering.
results/predictions/fasta/*.PRE.fasta: FASTA entries for predicted loci, including confidence label and seed annotations in the header.
results/predictions/heatmap/*.heatmap.csv: Summary table for downstream plotting with per-family total and filtered hit counts.

GFF Header Fields#

Header:

##gff-version 3
# MirMachine version: (MirMachine version used)
# CM Models: Built using MirGeneDB 3.0 (database version)
# Total families searched: (Total families searched for this run)
# Node: (Node name given)
# Model: (selected model)
# Genome file: (genome file location)
# Species: (species name given)
# Params: (Command line parameters)
# microRNA families searched: (searched families)
# Expected microRNA family losses: (microRNA family losses for this Node)
# microRNA score: (percent of score families with >=1 hit)
# microRNA seed score: (percent of score families with >=1 hit that has seed != None)
# microRNA hiconf seed score: (percent of score families with >=1 hit that has at least one * seed)

The filtered and unfiltered files each contain all three scores in the header.

Example GFF Row#

An example prediction line:

chrI        MirMachine      microRNA        9379947 9380005 57.4    -       .       gene_id=Mir-71.PRE;E-value=3e-10;sequence_with_30nt=TCACACACAGAGGTTGTCTGCTCTGAACGATGAAAGACATGGGTAGTGAGACGTCGGAGCCTCGTCGTATCACTATTCTGTTTTTCGCCGTCGGGATCGTGACCTGGAAGCTGTAAACT

Field meanings:

chrI: chromosome/contig name
MirMachine: annotation source
microRNA: feature type
9379947 and 9380005: start/end
57.4: CM bitscore
-: strand
gene_id: miRNA family ID
E-value: hit E-value
sequence_with_30nt: hit sequence with 30 nt flanks

Read about GFF3 file format

FASTA files#

Example FASTA of a prediction:

>Mir-9.PRE_chrI_9332963_9333028_(+)_56.8_HIGHconf_p5_seed(CTTTGGT)_p3_seed(AAAGCTA,TAAAGCT)
TCTTTGGTGATTCAGCTTCAATGATTGGCTACAGGTTTCTTTCATAAAGCTAGGTTACCAAAGCTC

Header pattern:

>family_chr_start_end_(strand)_bitscore_confidence_seed_annotations

Confidence values are HIGHconf or LOWconf.

Heatmap CSV#

results/predictions/heatmap/<species>.heatmap.csv includes metadata lines from the GFF header followed by a CSV table with this schema:

species,query_node,family,node,total_hits,filtered_hits,unfiltered_seed,filtered_seed,unfiltered_hiconf_seed,filtered_hiconf_seed

Output

Contents