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IsoSeq Annotation (Map + Collapse + SQANTI3)

Annotation: C57 I-K1 (individual)

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Type
Custom
Status
succeeded
Engine
custom
Duration
0.1 h
Source Data
Study Strain-specific cortex gene expression and isoform usage
Pipeline
PacBio CCS (Subreads → HiFi)
Run #74
succeeded
IsoSeq Clustering (Refine + Cluster)
Run #79
succeeded 1 sources
IsoSeq Annotation (Map + Collapse + SQANTI3)
Run #89 (this run)
succeeded 1 sources
Functional Annotation (TransDecoder + Pfam + SwissProt)
Run #99
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
8,032
Genes
5,494
FSM
5,971
ISM
678
NIC
685
NNC
595
Canonical SJ
92.4%

SQANTI3 Structural Categories

SQANTI3 Subcategories

Full-Length Read Support per Isoform

8,032 isoforms | Median FL: 1 | Mean FL: 1.4 | Max FL: 25

Transcript Length Distribution

8,032 transcripts | Median: 2,542 nt | Mean: 2,665 nt | N50: 3,163 nt

Exons per Transcript

Output Files

GMST
FileSize
GMST_tmp HPC 2.1 MB
GMST_tmp.faa HPC 4 MB
GMST_tmp.fnn HPC 11.3 MB
GeneMark_hmm.mod HPC 190.6 KB
gms.log HPC 17.8 KB
seq_bin_1 HPC 7.3 MB
seq_bin_1.mod HPC 63.4 KB
seq_bin_2 HPC 6.6 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 124.5 KB
Root
FileSize
collapsed.abundance.txt HPC 133.6 KB
collapsed.fasta HPC 20.9 MB
collapsed.flnc_count.txt HPC 94.1 KB
collapsed.gff HPC 7.7 MB
collapsed.group.txt HPC 253.6 KB
collapsed.read_stat.txt HPC 2.9 MB
collapsed.report.json HPC 702 B
mapped.bam HPC 7.9 MB
mapped.bam.bai HPC 1.3 MB
mouse_c57_i_k1.params.txt HPC 815 B
mouse_c57_i_k1_SQANTI3_report.html HPC 5.9 MB
mouse_c57_i_k1_classification.txt HPC 5.6 MB
mouse_c57_i_k1_corrected.faa HPC 3.9 MB
mouse_c57_i_k1_corrected.fasta HPC 20.8 MB
mouse_c57_i_k1_corrected.genePred HPC 2.3 MB
mouse_c57_i_k1_corrected.gtf HPC 7.7 MB
mouse_c57_i_k1_corrected.gtf.cds.gff HPC 16.2 MB
mouse_c57_i_k1_junctions.txt HPC 8.6 MB
refAnnotation_mouse_c57_i_k1.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_i_k1, Mus musculus GRCm39)
Started 2026-03-05T09:04:48+00:00
Completed 2026-03-04T23:10:23+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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            "name": "IsoSeq Annotation (mouse_c57_i_k1, Mus musculus GRCm39) \u2014 Run #89",
            "description": "IsoSeq post-clustering annotation: pbmm2 + isoseq collapse + SQANTI3",
            "datePublished": "2026-03-04",
            "license": {
                "@id": "https://creativecommons.org/licenses/by/4.0/"
            },
            "hasPart": [
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                    "@id": "mouse_c57_i_k1_junctions.txt"
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                {
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                {
                    "@id": "unknown_strand.gtf"
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                    "@id": "refAnnotation_mouse_c57_i_k1.genePred"
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                    "@id": "mouse_c57_i_k1_corrected.faa"
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                {
                    "@id": "mouse_c57_i_k1_corrected.fasta"
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                {
                    "@id": "mouse_c57_i_k1_classification.txt"
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                {
                    "@id": "mouse_c57_i_k1_corrected.gtf.cds.gff"
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                {
                    "@id": "mouse_c57_i_k1_SQANTI3_report.html"
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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": "GMST/seq_bin_2"
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        {
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            "name": "isoseq",
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            "url": {
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        },
        {
            "@id": "#sqanti3",
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            "name": "SQANTI3",
            "softwareVersion": "5.3.6",
            "url": {
                "@id": "https://github.com/ConesaLab/SQANTI3"
            }
        },
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            "name": "Singularity",
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            }
        },
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        {
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            "sha256": "c5e503db25c6d1d757bdb76fca81d4b5d7054b3c522b1c7cf52880827c2b54bb"
        },
        {
            "@id": "mouse_c57_i_k1_corrected.genePred",
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        {
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        {
            "@id": "mouse_c57_i_k1_corrected.fasta",
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        {
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        {
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        {
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            "name": "mapped.bam",
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        {
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        },
        {
            "@id": "#execution",
            "@type": "CreateAction",
            "name": "IsoSeq Annotation: pbmm2 + collapse + SQANTI3 (mouse_c57_i_k1, Mus musculus GRCm39)",
            "instrument": {
                "@id": "#pbmm2"
            },
            "startTime": "2026-03-05T09:04:48+00:00",
            "endTime": "2026-03-04T23:10:23+00:00",
            "result": [
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                    "@id": "mouse_c57_i_k1_junctions.txt"
                },
                {
                    "@id": "collapsed.fasta"
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                {
                    "@id": "mouse_c57_i_k1_corrected.genePred"
                },
                {
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                {
                    "@id": "collapsed.flnc_count.txt"
                },
                {
                    "@id": "mouse_c57_i_k1_corrected.gtf"
                },
                {
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                {
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                {
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                },
                {
                    "@id": "mouse_c57_i_k1_corrected.faa"
                },
                {
                    "@id": "mouse_c57_i_k1_corrected.fasta"
                },
                {
                    "@id": "mouse_c57_i_k1_classification.txt"
                },
                {
                    "@id": "mouse_c57_i_k1_corrected.gtf.cds.gff"
                },
                {
                    "@id": "mouse_c57_i_k1_SQANTI3_report.html"
                },
                {
                    "@id": "collapsed.report.json"
                },
                {
                    "@id": "collapsed.abundance.txt"
                },
                {
                    "@id": "mapped.bam"
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                {
                    "@id": "collapsed.group.txt"
                },
                {
                    "@id": "mouse_c57_i_k1.params.txt"
                },
                {
                    "@id": "collapsed.read_stat.txt"
                },
                {
                    "@id": "GMST/seq_bin_3"
                },
                {
                    "@id": "GMST/seq_bin_1"
                },
                {
                    "@id": "GMST/GMST_tmp.fnn"
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                {
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                },
                {
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                {
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                {
                    "@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": "c89784caad2354d4a0b4dbeee4914aaf590b787c7f9a268f07295fccfd8d55b5"
        }
    ]
}