ONT Long-Read Transcriptomics (IsoQuant)
Type
CWL
Status
succeeded
Engine
cwltool
Duration
6.2 h
Pipeline
ONT Long-Read Transcriptomics (IsoQuant)
Run #31
(this run)
succeeded
ONT Isoform Functional Annotation (superseded)
Workflow
ONT Transcriptomics -- Moth Pupa Body (H. armigera)
#cwl
Software Tools
| Tool | Version | URL |
|---|---|---|
| cwltool | - | https://github.com/common-workflow-language/cwltool |
Results Summary
Total Reads
6,212,805
Expressed Genes (CPM ≥ 1)
4,774
Novel Transcripts (CPM ≥ 1)
535
PolyA Detected
5.1%
rRNA Reads
92.2%
mRNA Genes (CPM ≥ 1)
8,691
mRNA Transcripts (CPM ≥ 1)
9,632
ORFs (mRNA only)
6,722
Expressed Transcript Sources (CPM ≥ 1, unique reads, rRNA excluded)
Novel Transcript Categories (CPM ≥ 1, unique reads, rRNA excluded)
Top Expressed Genes (CPM, unique reads)
All Reads (inc. rRNA)
mRNA Only (rRNA excluded)
Gene Expression Distribution (CPM, unique reads)
All Reads (inc. rRNA)
mRNA Only (rRNA excluded)
Read Assignment Quality
Read Structural Classification
Chromosomal Distribution (unique reads)
All Unique Reads
mRNA Reads Only
Gene Biotype Distribution (expressed genes, CPM ≥ 1, rRNA excluded)
Transcript Length Distribution (expressed transcripts, CPM ≥ 1, rRNA excluded)
6,878 transcripts | Median: 1,923 nt | Mean: 2,558 nt | N50: 3,401 nt
Exons per Transcript (expressed transcripts, CPM ≥ 1, rRNA excluded)
Isoforms per Gene (expressed transcripts, CPM ≥ 1, rRNA excluded)
TransDecoder ORF Types (expressed transcripts, rRNA excluded)
Peptide Length Distribution (expressed transcripts, rRNA excluded)
6,722 ORFs | Median: 388 aa | Mean: 522 aa | Max: 20,284 aa
Output Files
Input Data
| File | Format | Description |
|---|---|---|
OUT.transcript_models.gtf |
text/plain | - |
OUT.extended_annotation.gtf |
text/plain | - |
OUT.read_assignments.tsv.gz |
application/octet-stream | - |
OUT.transcript_counts.tsv |
text/tab-separated-values | - |
OUT.gene_counts.tsv |
text/tab-separated-values | - |
Provenance
| Execution | Expression quantification summary |
| Completed | 2026-02-27T11:00:28+00:00 |
RO-Crate 1.1
Workflow RO-Crate 1.0
FAIR
This analysis is packaged as a Research Object Crate
with machine-readable provenance and FAIR metadata.
RO-Crate Metadata (JSON-LD)
Show/hide raw JSON-LD
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"datePublished": "2026-02-27",
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"@id": "transcripts.fa.transdecoder.gff3"
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{
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"@id": "OUT.read_assignments.tsv.gz"
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{
"@id": "OUT.transcript_counts.tsv"
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{
"@id": "OUT.gene_counts.tsv"
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}