ONT Long-Read Transcriptomics (IsoQuant)
C57BL/6 combined (bc19+bc20+bc21) — GENCODE M35, complete_genedb
Type
CWL
Status
succeeded
Engine
cwltool
Duration
0.6 h
Source Data
| Study | Strain-specific cortex gene expression and isoform usage |
| Sample prep | PCR-cDNA barcoding library preparation for C57/DBA mouse RNA (SQK-PCB111.24) 2023-03-13 |
| Sample prep | AMPure XP 1.5 kb size selection of C57/DBA PCR-cDNA libraries 2023-05-01 |
| Sample prep | PCR-cDNA barcoding library preparation for C57/DBA mouse RNA (run 3, bc10-15) 2023-05-09 |
| Sequencing | Nanopore PCR-cDNA sequencing of C57/DBA mouse RNA (run 1) 2023-04-21 |
| Sequencing | Nanopore PCR-cDNA sequencing of C57/DBA mouse RNA 1.5kb (run 2) 2023-05-04 |
| Sequencing | Nanopore PCR-cDNA sequencing of C57/DBA mouse RNA (run 3) 2023-05-12 |
| Run Data | Run #61 (6 samples) |
| Run Data | Run #62 (6 samples) |
| Run Data | Run #63 (6 samples) |
| Samples | C57_rep1_bc10 C57_rep1_bc19 C57_rep1_bc19_1.5kb C57_rep2_bc11 C57_rep2_bc20 C57_rep2_bc20_1.5kb C57_rep3_bc12 C57_rep3_bc21 C57_rep3_bc21_1.5kb DBA_rep1_bc13 DBA_rep1_bc22 DBA_rep1_bc22_1.5kb DBA_rep2_bc14 DBA_rep2_bc23 DBA_rep2_bc23_1.5kb DBA_rep3_bc15 DBA_rep3_bc24 DBA_rep3_bc24_1.5kb |
Workflow
ONT Transcriptomics (IsoQuant + TransDecoder)
#cwl
Software Tools
| Tool | Version | URL |
|---|---|---|
| cwltool | - | https://github.com/common-workflow-language/cwltool |
| isoquant_3.6.0--hdfd78af_0.sif | - | - |
Results Summary
Total Reads
1,726,210
Expressed Genes (CPM ≥ 1)
13,315
Novel Transcripts (CPM ≥ 1)
1,709
PolyA Detected
85.7%
Expressed Transcript Sources (CPM ≥ 1, unique reads)
Novel Transcript Categories (CPM ≥ 1, unique reads)
Top Expressed Genes (CPM, unique reads)
Gene Expression Distribution (CPM, unique reads)
Read Assignment Quality
Read Structural Classification
Chromosomal Distribution (unique reads)
Transcript Length Distribution (expressed transcripts, CPM ≥ 1)
14,134 transcripts | Median: 1,828 nt | Mean: 2,248 nt | N50: 2,810 nt
Exons per Transcript (expressed transcripts, CPM ≥ 1)
Isoforms per Gene (expressed transcripts, CPM ≥ 1)
TransDecoder ORF Types (expressed transcripts)
Peptide Length Distribution (expressed transcripts)
14,709 ORFs | Median: 278 aa | Mean: 362 aa | Max: 6,299 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 | 2026-03-01T07:41:56+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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