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IsoSeq Annotation (Map + Collapse + SQANTI3)

Annotation: All 5 SMRT cells combined

Download ZIP JSON-LD
Type
Custom
Status
succeeded
Engine
custom
Duration
0.4 h
Source Data
Study Strain-specific cortex gene expression and isoform usage
Pipeline
PacBio CCS (Subreads → HiFi)
Run #74
succeeded
Run #75
succeeded
Run #76
succeeded
Run #77
succeeded
Run #78
succeeded
IsoSeq Clustering (Refine + Cluster)
Run #86
succeeded 5 sources
IsoSeq Annotation (Map + Collapse + SQANTI3)
Run #96 (this run)
succeeded 1 sources
Functional Annotation (TransDecoder + Pfam + SwissProt)
Run #106
succeeded 1 sources
Combined From

Software Tools

ToolVersionURL
pbmm2 1.13.0 https://github.com/PacificBiosciences/pbmm2
isoseq 4.0.0 https://github.com/PacificBiosciences/IsoSeq
SQANTI3 5.3.6 https://github.com/ConesaLab/SQANTI3
Singularity - https://sylabs.io/singularity/

Results Summary

Mapped Reads
0
Collapsed Isoforms
27,196
Genes
11,022
FSM
14,991
ISM
3,231
NIC
3,596
NNC
4,555
Canonical SJ
85.0%

SQANTI3 Structural Categories

SQANTI3 Subcategories

Full-Length Read Support per Isoform

27,196 isoforms | Median FL: 1 | Mean FL: 2.1 | Max FL: 57

Transcript Length Distribution

27,196 transcripts | Median: 2,568 nt | Mean: 2,745 nt | N50: 3,276 nt

Exons per Transcript

Output Files

GMST
FileSize
GMST_tmp HPC 7.1 MB
GMST_tmp.faa HPC 13.4 MB
GMST_tmp.fnn HPC 37.6 MB
GeneMark_hmm.mod HPC 190.6 KB
gms.log HPC 15.8 KB
seq_bin_1 HPC 26.8 MB
seq_bin_1.mod HPC 63.4 KB
seq_bin_2 HPC 23.2 MB
seq_bin_2.mod HPC 63.4 KB
seq_bin_3 HPC 21.8 MB
seq_bin_3.mod HPC 63.4 KB
RTS
FileSize
sj.rts.results.tsv HPC 448.9 KB
Root
FileSize
collapsed.abundance.txt HPC 462.3 KB
collapsed.fasta HPC 72.8 MB
collapsed.flnc_count.txt HPC 328.5 KB
collapsed.gff HPC 25.5 MB
collapsed.group.txt HPC 1.2 MB
collapsed.read_stat.txt HPC 21.9 MB
collapsed.report.json HPC 704 B
mapped.bam HPC 31.1 MB
mapped.bam.bai HPC 1.3 MB
mouse_all_5_smrt_cells_combined.params.txt HPC 832 B
mouse_all_5_smrt_cells_combined_SQANTI3_report.html HPC 7.6 MB
mouse_all_5_smrt_cells_combined_classification.txt HPC 18.8 MB
mouse_all_5_smrt_cells_combined_corrected.faa HPC 12.9 MB
mouse_all_5_smrt_cells_combined_corrected.fasta HPC 72.5 MB
mouse_all_5_smrt_cells_combined_corrected.genePred HPC 7.7 MB
mouse_all_5_smrt_cells_combined_corrected.gtf HPC 25.5 MB
mouse_all_5_smrt_cells_combined_corrected.gtf.cds.gff HPC 52.9 MB
mouse_all_5_smrt_cells_combined_junctions.txt HPC 28.5 MB
refAnnotation_mouse_all_5_smrt_cells_combined.genePred HPC 32.1 MB
results_summary.json HPC 2.5 KB
unknown_strand.gtf HPC 0 B

Provenance

Execution IsoSeq Annotation: pbmm2 + collapse + SQANTI3 (mouse_all_5_smrt_cells_combined, Mus musculus GRCm39)
Started 2026-03-05T09:05:41+00:00
Completed 2026-03-04T23:31:18+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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        {
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        {
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            "@type": "CreateAction",
            "name": "IsoSeq Annotation: pbmm2 + collapse + SQANTI3 (mouse_all_5_smrt_cells_combined, Mus musculus GRCm39)",
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            "startTime": "2026-03-05T09:05:41+00:00",
            "endTime": "2026-03-04T23:31:18+00:00",
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                {
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                {
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                {
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                {
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                {
                    "@id": "collapsed.group.txt"
                },
                {
                    "@id": "mouse_all_5_smrt_cells_combined_corrected.gtf"
                },
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                    "@id": "GMST/seq_bin_3"
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                    "@id": "GMST/seq_bin_1"
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                    "@id": "GMST/GeneMark_hmm.mod"
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                {
                    "@id": "GMST/seq_bin_2.mod"
                },
                {
                    "@id": "GMST/GMST_tmp"
                },
                {
                    "@id": "GMST/seq_bin_3.mod"
                },
                {
                    "@id": "GMST/seq_bin_1.mod"
                },
                {
                    "@id": "GMST/gms.log"
                },
                {
                    "@id": "GMST/GMST_tmp.faa"
                },
                {
                    "@id": "GMST/seq_bin_2"
                },
                {
                    "@id": "RTS/sj.rts.results.tsv"
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