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IsoSeq Annotation (Map + Collapse + SQANTI3)

Annotation: All 2017 combined (4 SMRT cells, excl. K7 2019)

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 #74
succeeded
Run #75
succeeded
Run #76
succeeded
Run #77
succeeded
IsoSeq Clustering (Refine + Cluster)
Run #88
succeeded 4 sources
IsoSeq Annotation (Map + Collapse + SQANTI3)
Run #98 (this run)
succeeded 1 sources
Functional Annotation (TransDecoder + Pfam + SwissProt)
Run #108
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
22,808
Genes
10,100
FSM
13,271
ISM
2,614
NIC
2,875
NNC
3,454
Canonical SJ
86.5%

SQANTI3 Structural Categories

SQANTI3 Subcategories

Full-Length Read Support per Isoform

22,808 isoforms | Median FL: 1 | Mean FL: 1.9 | Max FL: 53

Transcript Length Distribution

22,808 transcripts | Median: 2,615 nt | Mean: 2,795 nt | N50: 3,300 nt

Exons per Transcript

Output Files

GMST
FileSize
GMST_tmp HPC 5.9 MB
GMST_tmp.faa HPC 11.5 MB
GMST_tmp.fnn HPC 32.3 MB
GeneMark_hmm.mod HPC 190.6 KB
gms.log HPC 15.7 KB
seq_bin_1 HPC 23 MB
seq_bin_1.mod HPC 63.4 KB
seq_bin_2 HPC 19.7 MB
seq_bin_2.mod HPC 63.4 KB
seq_bin_3 HPC 18.5 MB
seq_bin_3.mod HPC 63.4 KB
RTS
FileSize
sj.rts.results.tsv HPC 374 KB
Root
FileSize
collapsed.abundance.txt HPC 384.9 KB
collapsed.fasta HPC 62.1 MB
collapsed.flnc_count.txt HPC 272.8 KB
collapsed.gff HPC 21.7 MB
collapsed.group.txt HPC 939.3 KB
collapsed.read_stat.txt HPC 15.9 MB
collapsed.report.json HPC 704 B
mapped.bam HPC 25.6 MB
mapped.bam.bai HPC 1.3 MB
mouse_all_2017.params.txt HPC 815 B
mouse_all_2017_SQANTI3_report.html HPC 7.2 MB
mouse_all_2017_classification.txt HPC 16 MB
mouse_all_2017_corrected.faa HPC 11.1 MB
mouse_all_2017_corrected.fasta HPC 61.9 MB
mouse_all_2017_corrected.genePred HPC 6.6 MB
mouse_all_2017_corrected.gtf HPC 21.7 MB
mouse_all_2017_corrected.gtf.cds.gff HPC 45.3 MB
mouse_all_2017_junctions.txt HPC 24.4 MB
refAnnotation_mouse_all_2017.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_2017, Mus musculus GRCm39)
Started 2026-03-05T09:40:18+00:00
Completed 2026-03-04T23:50:46+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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    "@context": "https://w3id.org/ro/crate/1.1/context",
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            "@type": "Dataset",
            "name": "IsoSeq Annotation (mouse_all_2017, Mus musculus GRCm39) \u2014 Run #98",
            "description": "IsoSeq post-clustering annotation: pbmm2 + isoseq collapse + SQANTI3",
            "datePublished": "2026-03-04",
            "license": {
                "@id": "https://creativecommons.org/licenses/by/4.0/"
            },
            "hasPart": [
                {
                    "@id": "collapsed.fasta"
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                {
                    "@id": "refAnnotation_mouse_all_2017.genePred"
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                {
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                },
                {
                    "@id": "mouse_all_2017_corrected.gtf"
                },
                {
                    "@id": "mouse_all_2017_SQANTI3_report.html"
                },
                {
                    "@id": "mouse_all_2017_junctions.txt"
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                {
                    "@id": "unknown_strand.gtf"
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                {
                    "@id": "collapsed.flnc_count.txt"
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                {
                    "@id": "collapsed.gff"
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                {
                    "@id": "mapped.bam.bai"
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                {
                    "@id": "mouse_all_2017_classification.txt"
                },
                {
                    "@id": "mouse_all_2017_corrected.fasta"
                },
                {
                    "@id": "collapsed.report.json"
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                {
                    "@id": "collapsed.abundance.txt"
                },
                {
                    "@id": "mapped.bam"
                },
                {
                    "@id": "mouse_all_2017.params.txt"
                },
                {
                    "@id": "collapsed.group.txt"
                },
                {
                    "@id": "mouse_all_2017_corrected.gtf.cds.gff"
                },
                {
                    "@id": "mouse_all_2017_corrected.faa"
                },
                {
                    "@id": "collapsed.read_stat.txt"
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                    "@id": "GMST/seq_bin_1"
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                {
                    "@id": "GMST/gms.log"
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                {
                    "@id": "GMST/GMST_tmp.faa"
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                {
                    "@id": "GMST/seq_bin_2"
                },
                {
                    "@id": "RTS/sj.rts.results.tsv"
                },
                {
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                }
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            }
        },
        {
            "@id": "#isoseq",
            "@type": "SoftwareApplication",
            "name": "isoseq",
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            "url": {
                "@id": "https://github.com/PacificBiosciences/IsoSeq"
            }
        },
        {
            "@id": "#sqanti3",
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            "name": "SQANTI3",
            "softwareVersion": "5.3.6",
            "url": {
                "@id": "https://github.com/ConesaLab/SQANTI3"
            }
        },
        {
            "@id": "#singularity",
            "@type": "SoftwareApplication",
            "name": "Singularity",
            "url": {
                "@id": "https://sylabs.io/singularity/"
            }
        },
        {
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        },
        {
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            "name": "mouse_all_2017_corrected.genePred",
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            "contentSize": "6.6 MB",
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        {
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        {
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            "name": "mouse_all_2017_SQANTI3_report.html",
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        {
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            "sha256": "0dd21648fccad8b2d2ed81a542ad87fd579f745b02636b2d179926fdc826c145"
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        {
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            "name": "unknown_strand.gtf",
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            "sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855"
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        {
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        {
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        {
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        {
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        {
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        {
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        {
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        {
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        {
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        {
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        },
        {
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        },
        {
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            "@type": "CreateAction",
            "name": "IsoSeq Annotation: pbmm2 + collapse + SQANTI3 (mouse_all_2017, Mus musculus GRCm39)",
            "instrument": {
                "@id": "#pbmm2"
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            "startTime": "2026-03-05T09:40:18+00:00",
            "endTime": "2026-03-04T23:50:46+00:00",
            "result": [
                {
                    "@id": "collapsed.fasta"
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                {
                    "@id": "refAnnotation_mouse_all_2017.genePred"
                },
                {
                    "@id": "mouse_all_2017_corrected.genePred"
                },
                {
                    "@id": "mouse_all_2017_corrected.gtf"
                },
                {
                    "@id": "mouse_all_2017_SQANTI3_report.html"
                },
                {
                    "@id": "mouse_all_2017_junctions.txt"
                },
                {
                    "@id": "unknown_strand.gtf"
                },
                {
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                {
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                {
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                {
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                },
                {
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                {
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                },
                {
                    "@id": "collapsed.abundance.txt"
                },
                {
                    "@id": "mapped.bam"
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                {
                    "@id": "mouse_all_2017.params.txt"
                },
                {
                    "@id": "collapsed.group.txt"
                },
                {
                    "@id": "mouse_all_2017_corrected.gtf.cds.gff"
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                    "@id": "mouse_all_2017_corrected.faa"
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                {
                    "@id": "collapsed.read_stat.txt"
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                {
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                {
                    "@id": "GMST/seq_bin_1"
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                {
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                    "@id": "GMST/seq_bin_1.mod"
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                {
                    "@id": "GMST/gms.log"
                },
                {
                    "@id": "GMST/GMST_tmp.faa"
                },
                {
                    "@id": "GMST/seq_bin_2"
                },
                {
                    "@id": "RTS/sj.rts.results.tsv"
                }
            ]
        },
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            "description": "SQANTI3 structural classification summary",
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            "sha256": "97335588e0bd55f2942b94413ce703fa763a9c8e7fc32d2bca41835b25f79062"
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    ]
}