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IsoSeq Annotation (Map + Collapse + SQANTI3)

Annotation: DBA K7-50pM (individual)

Download ZIP JSON-LD
Type
Custom
Status
succeeded
Engine
custom
Duration
0.2 h
Source Data
Study Strain-specific cortex gene expression and isoform usage
Pipeline
PacBio CCS (Subreads → HiFi)
Run #77
succeeded
IsoSeq Clustering (Refine + Cluster)
Run #82
succeeded 1 sources
IsoSeq Annotation (Map + Collapse + SQANTI3)
Run #92 (this run)
succeeded 1 sources
Functional Annotation (TransDecoder + Pfam + SwissProt)
Run #102
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
10,575
Genes
6,585
FSM
7,177
ISM
1,026
NIC
972
NNC
1,227
Canonical SJ
87.8%

SQANTI3 Structural Categories

SQANTI3 Subcategories

Full-Length Read Support per Isoform

10,575 isoforms | Median FL: 1 | Mean FL: 1.5 | Max FL: 27

Transcript Length Distribution

10,575 transcripts | Median: 2,508 nt | Mean: 2,681 nt | N50: 3,107 nt

Exons per Transcript

Output Files

GMST
FileSize
GMST_tmp HPC 2.8 MB
GMST_tmp.faa HPC 5.3 MB
GMST_tmp.fnn HPC 14.8 MB
GeneMark_hmm.mod HPC 190.6 KB
gms.log HPC 15.7 KB
seq_bin_1 HPC 9.7 MB
seq_bin_1.mod HPC 63.4 KB
seq_bin_2 HPC 8.8 MB
seq_bin_2.mod HPC 63.4 KB
seq_bin_3 HPC 8.7 MB
seq_bin_3.mod HPC 63.4 KB
RTS
FileSize
sj.rts.results.tsv HPC 181.2 KB
Root
FileSize
collapsed.abundance.txt HPC 176.6 KB
collapsed.fasta HPC 27.7 MB
collapsed.flnc_count.txt HPC 124.6 KB
collapsed.gff HPC 10 MB
collapsed.group.txt HPC 353.4 KB
collapsed.read_stat.txt HPC 4.5 MB
collapsed.report.json HPC 703 B
mapped.bam HPC 10.7 MB
mapped.bam.bai HPC 1.3 MB
mouse_dba_k7_50pm.params.txt HPC 818 B
mouse_dba_k7_50pm_SQANTI3_report.html HPC 6.1 MB
mouse_dba_k7_50pm_classification.txt HPC 7.4 MB
mouse_dba_k7_50pm_corrected.faa HPC 5.1 MB
mouse_dba_k7_50pm_corrected.fasta HPC 27.5 MB
mouse_dba_k7_50pm_corrected.genePred HPC 3 MB
mouse_dba_k7_50pm_corrected.gtf HPC 10 MB
mouse_dba_k7_50pm_corrected.gtf.cds.gff HPC 21.1 MB
mouse_dba_k7_50pm_junctions.txt HPC 11.2 MB
refAnnotation_mouse_dba_k7_50pm.genePred HPC 32.1 MB
results_summary.json HPC 2.4 KB
unknown_strand.gtf HPC 0 B

Provenance

Execution IsoSeq Annotation: pbmm2 + collapse + SQANTI3 (mouse_dba_k7_50pm, Mus musculus GRCm39)
Started 2026-03-05T09:05:11+00:00
Completed 2026-03-04T23:16:44+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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            "description": "IsoSeq post-clustering annotation: pbmm2 + isoseq collapse + SQANTI3",
            "datePublished": "2026-03-04",
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                    "@id": "mouse_dba_k7_50pm_corrected.genePred"
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        {
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            "@type": "CreateAction",
            "name": "IsoSeq Annotation: pbmm2 + collapse + SQANTI3 (mouse_dba_k7_50pm, Mus musculus GRCm39)",
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            "startTime": "2026-03-05T09:05:11+00:00",
            "endTime": "2026-03-04T23:16:44+00:00",
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                {
                    "@id": "collapsed.abundance.txt"
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                {
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                {
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                {
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                {
                    "@id": "GMST/GMST_tmp.faa"
                },
                {
                    "@id": "GMST/seq_bin_2"
                },
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            ]
        },
        {
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            "name": "results_summary.json",
            "description": "SQANTI3 structural classification summary",
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            "sha256": "fa4e4272e41b46bd14f4e41676638268dff066d0ec75ffdae32b82384e5712ef"
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    ]
}