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IsoSeq Annotation (Map + Collapse + SQANTI3)

Annotation: DBA K7 (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 #78
succeeded
IsoSeq Clustering (Refine + Cluster)
Run #83
succeeded 1 sources
IsoSeq Annotation (Map + Collapse + SQANTI3)
Run #93 (this run)
succeeded 1 sources
Functional Annotation (TransDecoder + Pfam + SwissProt)
Run #103
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
10,397
Genes
6,616
FSM
7,079
ISM
1,167
NIC
858
NNC
1,070
Canonical SJ
86.5%

SQANTI3 Structural Categories

SQANTI3 Subcategories

Full-Length Read Support per Isoform

10,397 isoforms | Median FL: 1 | Mean FL: 1.6 | Max FL: 51

Transcript Length Distribution

10,397 transcripts | Median: 2,189 nt | Mean: 2,372 nt | N50: 2,928 nt

Exons per Transcript

Output Files

GMST
FileSize
GMST_tmp HPC 2.7 MB
GMST_tmp.faa HPC 4.6 MB
GMST_tmp.fnn HPC 13 MB
GeneMark_hmm.mod HPC 190.6 KB
gms.log HPC 15.7 KB
seq_bin_1 HPC 7.9 MB
seq_bin_1.mod HPC 63.4 KB
seq_bin_2 HPC 9.1 MB
seq_bin_2.mod HPC 63.4 KB
seq_bin_3 HPC 6.7 MB
seq_bin_3.mod HPC 63.4 KB
RTS
FileSize
sj.rts.results.tsv HPC 158.1 KB
Root
FileSize
collapsed.abundance.txt HPC 173.7 KB
collapsed.fasta HPC 24.1 MB
collapsed.flnc_count.txt HPC 122.6 KB
collapsed.gff HPC 9.1 MB
collapsed.group.txt HPC 364 KB
collapsed.read_stat.txt HPC 4.8 MB
collapsed.report.json HPC 703 B
mapped.bam HPC 9.5 MB
mapped.bam.bai HPC 1.3 MB
mouse_dba_k7.params.txt HPC 813 B
mouse_dba_k7_SQANTI3_report.html HPC 6.1 MB
mouse_dba_k7_classification.txt HPC 6.7 MB
mouse_dba_k7_corrected.faa HPC 4.5 MB
mouse_dba_k7_corrected.fasta HPC 24 MB
mouse_dba_k7_corrected.genePred HPC 2.8 MB
mouse_dba_k7_corrected.gtf HPC 9.1 MB
mouse_dba_k7_corrected.gtf.cds.gff HPC 18.9 MB
mouse_dba_k7_junctions.txt HPC 10 MB
refAnnotation_mouse_dba_k7.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, Mus musculus GRCm39)
Started 2026-03-05T09:05:18+00:00
Completed 2026-03-04T23:18:33+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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            "@type": "Dataset",
            "name": "IsoSeq Annotation (mouse_dba_k7, Mus musculus GRCm39) \u2014 Run #93",
            "description": "IsoSeq post-clustering annotation: pbmm2 + isoseq collapse + SQANTI3",
            "datePublished": "2026-03-04",
            "license": {
                "@id": "https://creativecommons.org/licenses/by/4.0/"
            },
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                    "@id": "mouse_dba_k7_corrected.gtf"
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                    "@id": "mouse_dba_k7_classification.txt"
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                    "@id": "collapsed.fasta"
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                    "@id": "mouse_dba_k7_corrected.gtf.cds.gff"
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                {
                    "@id": "mouse_dba_k7_corrected.genePred"
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                {
                    "@id": "unknown_strand.gtf"
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                    "@id": "mouse_dba_k7_junctions.txt"
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                    "@id": "collapsed.flnc_count.txt"
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                    "@id": "mouse_dba_k7_SQANTI3_report.html"
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                    "@id": "collapsed.gff"
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                    "@id": "mapped.bam.bai"
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                    "@id": "mouse_dba_k7.params.txt"
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                    "@id": "collapsed.report.json"
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                {
                    "@id": "collapsed.abundance.txt"
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                {
                    "@id": "mapped.bam"
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                    "@id": "collapsed.group.txt"
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                {
                    "@id": "mouse_dba_k7_corrected.fasta"
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                    "@id": "GMST/GMST_tmp.faa"
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                {
                    "@id": "GMST/seq_bin_2"
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                    "@id": "RTS/sj.rts.results.tsv"
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        },
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            "name": "isoseq",
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            "url": {
                "@id": "https://github.com/PacificBiosciences/IsoSeq"
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        },
        {
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            "name": "SQANTI3",
            "softwareVersion": "5.3.6",
            "url": {
                "@id": "https://github.com/ConesaLab/SQANTI3"
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        },
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            "sha256": "ce9202d6753b39ab3debc4ccbcd9d8be922d1d7dbf3033f69157d07b3fc80469"
        },
        {
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        {
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        {
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        {
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            "sha256": "e412df714d9f11ef43a5995faccc68ab4ab6d55143772a535204fbaae6a37cd5"
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        {
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        {
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            "@id": "mapped.bam",
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        {
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            "@type": "CreateAction",
            "name": "IsoSeq Annotation: pbmm2 + collapse + SQANTI3 (mouse_dba_k7, Mus musculus GRCm39)",
            "instrument": {
                "@id": "#pbmm2"
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            "startTime": "2026-03-05T09:05:18+00:00",
            "endTime": "2026-03-04T23:18:33+00:00",
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                    "@id": "mouse_dba_k7_corrected.gtf"
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                {
                    "@id": "mouse_dba_k7_classification.txt"
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                {
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                {
                    "@id": "mouse_dba_k7_corrected.gtf.cds.gff"
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                {
                    "@id": "mouse_dba_k7_corrected.genePred"
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                {
                    "@id": "unknown_strand.gtf"
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                {
                    "@id": "mouse_dba_k7_junctions.txt"
                },
                {
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                },
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                {
                    "@id": "collapsed.gff"
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                {
                    "@id": "mapped.bam.bai"
                },
                {
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                },
                {
                    "@id": "refAnnotation_mouse_dba_k7.genePred"
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                {
                    "@id": "collapsed.report.json"
                },
                {
                    "@id": "collapsed.abundance.txt"
                },
                {
                    "@id": "mapped.bam"
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                {
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                {
                    "@id": "mouse_dba_k7_corrected.fasta"
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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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            "sha256": "0755aa90e7cf72d36d327d8f18d5abd0edb78df5f0001140328c30968d201db5"
        }
    ]
}