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IsoSeq Annotation (Map + Collapse + SQANTI3)

Annotation: C57 combined (I-K1 + K1-50pM)

Download ZIP JSON-LD
Type
Custom
Status
succeeded
Engine
custom
Duration
0.3 h
Source Data
Study Strain-specific cortex gene expression and isoform usage
Pipeline
PacBio CCS (Subreads → HiFi)
Run #74
succeeded
Run #76
succeeded
IsoSeq Clustering (Refine + Cluster)
Run #84
succeeded 2 sources
IsoSeq Annotation (Map + Collapse + SQANTI3)
Run #94 (this run)
succeeded 1 sources
Functional Annotation (TransDecoder + Pfam + SwissProt)
Run #104
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
14,069
Genes
7,890
FSM
9,489
ISM
1,436
NIC
1,514
NNC
1,387
Canonical SJ
90.9%

SQANTI3 Structural Categories

SQANTI3 Subcategories

Full-Length Read Support per Isoform

14,069 isoforms | Median FL: 1 | Mean FL: 1.6 | Max FL: 39

Transcript Length Distribution

14,069 transcripts | Median: 2,535 nt | Mean: 2,704 nt | N50: 3,203 nt

Exons per Transcript

Output Files

GMST
FileSize
GMST_tmp HPC 3.7 MB
GMST_tmp.faa HPC 7 MB
GMST_tmp.fnn HPC 19.7 MB
GeneMark_hmm.mod HPC 190.6 KB
gms.log HPC 15.7 KB
seq_bin_1 HPC 13.3 MB
seq_bin_1.mod HPC 63.4 KB
seq_bin_2 HPC 11.8 MB
seq_bin_2.mod HPC 63.4 KB
seq_bin_3 HPC 11.4 MB
seq_bin_3.mod HPC 63.4 KB
RTS
FileSize
sj.rts.results.tsv HPC 209.6 KB
Root
FileSize
collapsed.abundance.txt HPC 235.9 KB
collapsed.fasta HPC 37.1 MB
collapsed.flnc_count.txt HPC 166.8 KB
collapsed.gff HPC 13.3 MB
collapsed.group.txt HPC 508.3 KB
collapsed.read_stat.txt HPC 7.2 MB
collapsed.report.json HPC 703 B
mapped.bam HPC 14.5 MB
mapped.bam.bai HPC 1.3 MB
mouse_c57_combined.params.txt HPC 819 B
mouse_c57_combined_SQANTI3_report.html HPC 6.4 MB
mouse_c57_combined_classification.txt HPC 9.8 MB
mouse_c57_combined_corrected.faa HPC 6.8 MB
mouse_c57_combined_corrected.fasta HPC 37 MB
mouse_c57_combined_corrected.genePred HPC 4 MB
mouse_c57_combined_corrected.gtf HPC 13.3 MB
mouse_c57_combined_corrected.gtf.cds.gff HPC 28 MB
mouse_c57_combined_junctions.txt HPC 15 MB
refAnnotation_mouse_c57_combined.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_c57_combined, Mus musculus GRCm39)
Started 2026-03-05T09:05:26+00:00
Completed 2026-03-04T23:26:05+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 
{
    "@context": "https://w3id.org/ro/crate/1.1/context",
    "@graph": [
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            "@id": "ro-crate-metadata.json",
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                    "@id": "https://w3id.org/ro/crate/1.1"
                },
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                }
            ]
        },
        {
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            "@type": "Dataset",
            "name": "IsoSeq Annotation (mouse_c57_combined, Mus musculus GRCm39) \u2014 Run #94",
            "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": "mouse_c57_combined_corrected.faa"
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                {
                    "@id": "mouse_c57_combined_corrected.gtf.cds.gff"
                },
                {
                    "@id": "mouse_c57_combined.params.txt"
                },
                {
                    "@id": "mouse_c57_combined_junctions.txt"
                },
                {
                    "@id": "mouse_c57_combined_corrected.gtf"
                },
                {
                    "@id": "unknown_strand.gtf"
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                {
                    "@id": "collapsed.flnc_count.txt"
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                {
                    "@id": "mouse_c57_combined_corrected.fasta"
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                {
                    "@id": "collapsed.gff"
                },
                {
                    "@id": "mapped.bam.bai"
                },
                {
                    "@id": "mouse_c57_combined_classification.txt"
                },
                {
                    "@id": "refAnnotation_mouse_c57_combined.genePred"
                },
                {
                    "@id": "mouse_c57_combined_corrected.genePred"
                },
                {
                    "@id": "collapsed.report.json"
                },
                {
                    "@id": "collapsed.abundance.txt"
                },
                {
                    "@id": "mapped.bam"
                },
                {
                    "@id": "mouse_c57_combined_SQANTI3_report.html"
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                {
                    "@id": "collapsed.group.txt"
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                {
                    "@id": "collapsed.read_stat.txt"
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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_3.mod"
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                {
                    "@id": "GMST/seq_bin_1.mod"
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                {
                    "@id": "GMST/gms.log"
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                {
                    "@id": "GMST/GMST_tmp.faa"
                },
                {
                    "@id": "GMST/seq_bin_2"
                },
                {
                    "@id": "RTS/sj.rts.results.tsv"
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                }
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        },
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            "name": "pbmm2",
            "softwareVersion": "1.13.0",
            "url": {
                "@id": "https://github.com/PacificBiosciences/pbmm2"
            }
        },
        {
            "@id": "#isoseq",
            "@type": "SoftwareApplication",
            "name": "isoseq",
            "softwareVersion": "4.0.0",
            "url": {
                "@id": "https://github.com/PacificBiosciences/IsoSeq"
            }
        },
        {
            "@id": "#sqanti3",
            "@type": "SoftwareApplication",
            "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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            "name": "mouse_c57_combined_corrected.faa",
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            "contentSize": "6.8 MB",
            "sha256": "b7dae69b3df68e0133d3e40042108823c6db20377a597fcacdde6d1033fe4e65"
        },
        {
            "@id": "mouse_c57_combined_corrected.gtf.cds.gff",
            "@type": "File",
            "name": "mouse_c57_combined_corrected.gtf.cds.gff",
            "encodingFormat": "text/plain",
            "contentSize": "28 MB",
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        },
        {
            "@id": "mouse_c57_combined.params.txt",
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            "name": "mouse_c57_combined.params.txt",
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            "sha256": "a82209777f8873fb0d36468c4baef7220bdb626cc28f643dd0f2ebf049280481"
        },
        {
            "@id": "mouse_c57_combined_junctions.txt",
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            "name": "mouse_c57_combined_junctions.txt",
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            "contentSize": "15 MB",
            "sha256": "634a420d1a452a38bbdacd9fbbdb44e0efc671475e8909ff967eab8b8d120065"
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            "sha256": "dc2c50b75582169ab83ee2911c765585cbc05e0d03b1450c1c3d4835442e1957"
        },
        {
            "@id": "unknown_strand.gtf",
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            "name": "unknown_strand.gtf",
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            "sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855"
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            "name": "collapsed.flnc_count.txt",
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        {
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            "name": "mouse_c57_combined_corrected.fasta",
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            "sha256": "eb0b2ead415ebe669a62885f4841d82fe6a525c217d5db47569d9fca39d67dc7"
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        {
            "@id": "collapsed.gff",
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            "name": "collapsed.gff",
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            "contentSize": "13.3 MB",
            "sha256": "2f762b84fff8e97295b65be2b613a59bd061f5e9a995da4c37bc297a9d2fd68d"
        },
        {
            "@id": "mapped.bam.bai",
            "@type": "File",
            "name": "mapped.bam.bai",
            "encodingFormat": "application/octet-stream",
            "contentSize": "1.3 MB",
            "sha256": "e26b4f01baefedfb67abc1626c17f5b9cc07ad78283f89f744599d859005733a"
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        {
            "@id": "mouse_c57_combined_classification.txt",
            "@type": "File",
            "name": "mouse_c57_combined_classification.txt",
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            "contentSize": "9.8 MB",
            "sha256": "3755005ada184cb0d1c42acaf8469deec22237022c75a882ce7e9ba34eadc875"
        },
        {
            "@id": "refAnnotation_mouse_c57_combined.genePred",
            "@type": "File",
            "name": "refAnnotation_mouse_c57_combined.genePred",
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            "sha256": "e3c5e1e2e667a48d43c86d2cb73bf4854244771eff3cc194208a21ab44ca8c30"
        },
        {
            "@id": "collapsed.report.json",
            "@type": "File",
            "name": "collapsed.report.json",
            "encodingFormat": "application/json",
            "contentSize": "703 B",
            "sha256": "160758129a114fba370c78878a7b9828d0f3935b853deb7fc4f35619636cd64a"
        },
        {
            "@id": "collapsed.abundance.txt",
            "@type": "File",
            "name": "collapsed.abundance.txt",
            "encodingFormat": "text/plain",
            "contentSize": "235.9 KB",
            "sha256": "763d0a6679ea3ea3fd45e3097bb574b3ebf1fb7f97cbfa2d5630c088c1df680b"
        },
        {
            "@id": "mapped.bam",
            "@type": "File",
            "name": "mapped.bam",
            "encodingFormat": "application/octet-stream",
            "contentSize": "14.5 MB",
            "sha256": "71b65b1044d0d38670f2197e83dd21cb831d74cb4be1f9307863fe34d54c9a79"
        },
        {
            "@id": "mouse_c57_combined_SQANTI3_report.html",
            "@type": "File",
            "name": "mouse_c57_combined_SQANTI3_report.html",
            "encodingFormat": "text/html",
            "contentSize": "6.4 MB",
            "sha256": "fb7afdbeaf35d29789c4e1aae3ef026c21c0669f746c41cb8eae6ec5fc92fe5f"
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        {
            "@id": "collapsed.group.txt",
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            "name": "collapsed.group.txt",
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            "sha256": "4675980aa053b4da74a7956b33799bd7667345360b0b4793e7bd1bc7de8c1958"
        },
        {
            "@id": "collapsed.read_stat.txt",
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            "name": "collapsed.read_stat.txt",
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            "contentSize": "7.2 MB",
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        {
            "@id": "GMST/seq_bin_3",
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            "name": "seq_bin_3",
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        },
        {
            "@id": "GMST/seq_bin_1",
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            "name": "seq_bin_1",
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        },
        {
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            "name": "GMST_tmp.fnn",
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            "contentSize": "19.7 MB",
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        },
        {
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            "name": "GeneMark_hmm.mod",
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            "sha256": "2a141d1a00766143872fafd50a37ddcab2bc8e4d2c536d688fa0ac78cb3871b6"
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            "contentSize": "7 MB",
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            "sha256": "f8342123cb548d8ad70304d11af921da8efc62c147d117d11737235cd6670d66"
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        {
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        },
        {
            "@id": "#execution",
            "@type": "CreateAction",
            "name": "IsoSeq Annotation: pbmm2 + collapse + SQANTI3 (mouse_c57_combined, Mus musculus GRCm39)",
            "instrument": {
                "@id": "#pbmm2"
            },
            "startTime": "2026-03-05T09:05:26+00:00",
            "endTime": "2026-03-04T23:26:05+00:00",
            "result": [
                {
                    "@id": "collapsed.fasta"
                },
                {
                    "@id": "mouse_c57_combined_corrected.faa"
                },
                {
                    "@id": "mouse_c57_combined_corrected.gtf.cds.gff"
                },
                {
                    "@id": "mouse_c57_combined.params.txt"
                },
                {
                    "@id": "mouse_c57_combined_junctions.txt"
                },
                {
                    "@id": "mouse_c57_combined_corrected.gtf"
                },
                {
                    "@id": "unknown_strand.gtf"
                },
                {
                    "@id": "collapsed.flnc_count.txt"
                },
                {
                    "@id": "mouse_c57_combined_corrected.fasta"
                },
                {
                    "@id": "collapsed.gff"
                },
                {
                    "@id": "mapped.bam.bai"
                },
                {
                    "@id": "mouse_c57_combined_classification.txt"
                },
                {
                    "@id": "refAnnotation_mouse_c57_combined.genePred"
                },
                {
                    "@id": "mouse_c57_combined_corrected.genePred"
                },
                {
                    "@id": "collapsed.report.json"
                },
                {
                    "@id": "collapsed.abundance.txt"
                },
                {
                    "@id": "mapped.bam"
                },
                {
                    "@id": "mouse_c57_combined_SQANTI3_report.html"
                },
                {
                    "@id": "collapsed.group.txt"
                },
                {
                    "@id": "collapsed.read_stat.txt"
                },
                {
                    "@id": "GMST/seq_bin_3"
                },
                {
                    "@id": "GMST/seq_bin_1"
                },
                {
                    "@id": "GMST/GMST_tmp.fnn"
                },
                {
                    "@id": "GMST/GeneMark_hmm.mod"
                },
                {
                    "@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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            "@type": "File",
            "name": "results_summary.json",
            "description": "SQANTI3 structural classification summary",
            "encodingFormat": "application/json",
            "contentSize": "2.4 KB",
            "sha256": "617b6e7c6e99105f149f99198eca09e632ff840e05502038715ae0eadcccd46a"
        }
    ]
}