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IsoSeq Annotation (Map + Collapse + SQANTI3)

Annotation: DBA combined (I-K2 + K7-50pM + K7)

Download ZIP JSON-LD
Type
Custom
Status
succeeded
Engine
custom
Duration
0.4 h
Source Data
Study Strain-specific cortex gene expression and isoform usage
Pipeline
PacBio CCS (Subreads → HiFi)
Run #75
succeeded
Run #77
succeeded
Run #78
succeeded
IsoSeq Clustering (Refine + Cluster)
Run #85
succeeded 3 sources
IsoSeq Annotation (Map + Collapse + SQANTI3)
Run #95 (this run)
succeeded 1 sources
Functional Annotation (TransDecoder + Pfam + SwissProt)
Run #105
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
20,186
Genes
9,660
FSM
11,814
ISM
2,356
NIC
2,380
NNC
3,078
Canonical SJ
85.0%

SQANTI3 Structural Categories

SQANTI3 Subcategories

Full-Length Read Support per Isoform

20,186 isoforms | Median FL: 1 | Mean FL: 1.9 | Max FL: 71

Transcript Length Distribution

20,186 transcripts | Median: 2,518 nt | Mean: 2,686 nt | N50: 3,215 nt

Exons per Transcript

Output Files

GMST
FileSize
GMST_tmp HPC 5.2 MB
GMST_tmp.faa HPC 9.9 MB
GMST_tmp.fnn HPC 27.7 MB
GeneMark_hmm.mod HPC 190.6 KB
gms.log HPC 15.7 KB
seq_bin_1 HPC 19 MB
seq_bin_1.mod HPC 63.4 KB
seq_bin_2 HPC 16.8 MB
seq_bin_2.mod HPC 63.4 KB
seq_bin_3 HPC 16.3 MB
seq_bin_3.mod HPC 63.4 KB
RTS
FileSize
sj.rts.results.tsv HPC 343.7 KB
Root
FileSize
collapsed.abundance.txt HPC 340 KB
collapsed.fasta HPC 52.9 MB
collapsed.flnc_count.txt HPC 240.8 KB
collapsed.gff HPC 18.7 MB
collapsed.group.txt HPC 824.9 KB
collapsed.read_stat.txt HPC 13.5 MB
collapsed.report.json HPC 703 B
mapped.bam HPC 21.8 MB
mapped.bam.bai HPC 1.3 MB
mouse_dba_combined.params.txt HPC 819 B
mouse_dba_combined_SQANTI3_report.html HPC 7 MB
mouse_dba_combined_classification.txt HPC 13.9 MB
mouse_dba_combined_corrected.faa HPC 9.5 MB
mouse_dba_combined_corrected.fasta HPC 52.7 MB
mouse_dba_combined_corrected.genePred HPC 5.7 MB
mouse_dba_combined_corrected.gtf HPC 18.7 MB
mouse_dba_combined_corrected.gtf.cds.gff HPC 39 MB
mouse_dba_combined_junctions.txt HPC 20.9 MB
refAnnotation_mouse_dba_combined.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_dba_combined, Mus musculus GRCm39)
Started 2026-03-05T09:05:33+00:00
Completed 2026-03-04T23:28:33+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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    "@context": "https://w3id.org/ro/crate/1.1/context",
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            "name": "IsoSeq Annotation (mouse_dba_combined, Mus musculus GRCm39) \u2014 Run #95",
            "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": "collapsed.fasta"
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                    "@id": "mouse_dba_combined_SQANTI3_report.html"
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                    "@id": "refAnnotation_mouse_dba_combined.genePred"
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                {
                    "@id": "mouse_dba_combined_corrected.fasta"
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                    "@id": "mouse_dba_combined_corrected.gtf.cds.gff"
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                {
                    "@id": "mouse_dba_combined_classification.txt"
                },
                {
                    "@id": "unknown_strand.gtf"
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                    "@id": "mouse_dba_combined_junctions.txt"
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                    "@id": "collapsed.flnc_count.txt"
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                {
                    "@id": "collapsed.gff"
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                {
                    "@id": "mouse_dba_combined_corrected.faa"
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                {
                    "@id": "mapped.bam.bai"
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                {
                    "@id": "mouse_dba_combined.params.txt"
                },
                {
                    "@id": "collapsed.report.json"
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                {
                    "@id": "collapsed.abundance.txt"
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                {
                    "@id": "mouse_dba_combined_corrected.gtf"
                },
                {
                    "@id": "mapped.bam"
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                {
                    "@id": "collapsed.group.txt"
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                    "@id": "mouse_dba_combined_corrected.genePred"
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                    "@id": "collapsed.read_stat.txt"
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                    "@id": "GMST/gms.log"
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                    "@id": "GMST/GMST_tmp.faa"
                },
                {
                    "@id": "GMST/seq_bin_2"
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                    "@id": "RTS/sj.rts.results.tsv"
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            }
        },
        {
            "@id": "#isoseq",
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            "name": "isoseq",
            "softwareVersion": "4.0.0",
            "url": {
                "@id": "https://github.com/PacificBiosciences/IsoSeq"
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        },
        {
            "@id": "#sqanti3",
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            "name": "SQANTI3",
            "softwareVersion": "5.3.6",
            "url": {
                "@id": "https://github.com/ConesaLab/SQANTI3"
            }
        },
        {
            "@id": "#singularity",
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                "@id": "https://sylabs.io/singularity/"
            }
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        {
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            "name": "mouse_dba_combined_SQANTI3_report.html",
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            "contentSize": "7 MB",
            "sha256": "1008209f57b66032f494904a64a4bc04d0d70155218e8b04a649aa9060f06015"
        },
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            "name": "refAnnotation_mouse_dba_combined.genePred",
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        {
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        {
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        {
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            "@id": "collapsed.gff",
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        {
            "@id": "mouse_dba_combined_corrected.faa",
            "@type": "File",
            "name": "mouse_dba_combined_corrected.faa",
            "encodingFormat": "text/plain",
            "contentSize": "9.5 MB",
            "sha256": "59b3b6ca1c08dea1b2baa7792944eb90eeb2636e5f825989c6ee94aeab66a0e8"
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        {
            "@id": "mouse_dba_combined.params.txt",
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        {
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            "name": "collapsed.abundance.txt",
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            "contentSize": "340 KB",
            "sha256": "db94e1db7aa9356c7cb4062db65e6aa686acfd099e28afab76de1fb284eadada"
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        {
            "@id": "mouse_dba_combined_corrected.gtf",
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        {
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            "name": "mapped.bam",
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            "contentSize": "21.8 MB",
            "sha256": "d7f5cdc3f40c8d085ded0e25e8f03a280d96acecd9e2390ddc24136b29e11309"
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        {
            "@id": "collapsed.group.txt",
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        {
            "@id": "mouse_dba_combined_corrected.genePred",
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        },
        {
            "@id": "#execution",
            "@type": "CreateAction",
            "name": "IsoSeq Annotation: pbmm2 + collapse + SQANTI3 (mouse_dba_combined, Mus musculus GRCm39)",
            "instrument": {
                "@id": "#pbmm2"
            },
            "startTime": "2026-03-05T09:05:33+00:00",
            "endTime": "2026-03-04T23:28:33+00:00",
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                {
                    "@id": "collapsed.fasta"
                },
                {
                    "@id": "mouse_dba_combined_SQANTI3_report.html"
                },
                {
                    "@id": "refAnnotation_mouse_dba_combined.genePred"
                },
                {
                    "@id": "mouse_dba_combined_corrected.fasta"
                },
                {
                    "@id": "mouse_dba_combined_corrected.gtf.cds.gff"
                },
                {
                    "@id": "mouse_dba_combined_classification.txt"
                },
                {
                    "@id": "unknown_strand.gtf"
                },
                {
                    "@id": "mouse_dba_combined_junctions.txt"
                },
                {
                    "@id": "collapsed.flnc_count.txt"
                },
                {
                    "@id": "collapsed.gff"
                },
                {
                    "@id": "mouse_dba_combined_corrected.faa"
                },
                {
                    "@id": "mapped.bam.bai"
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                {
                    "@id": "mouse_dba_combined.params.txt"
                },
                {
                    "@id": "collapsed.report.json"
                },
                {
                    "@id": "collapsed.abundance.txt"
                },
                {
                    "@id": "mouse_dba_combined_corrected.gtf"
                },
                {
                    "@id": "mapped.bam"
                },
                {
                    "@id": "collapsed.group.txt"
                },
                {
                    "@id": "mouse_dba_combined_corrected.genePred"
                },
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                    "@id": "GMST/seq_bin_1"
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                {
                    "@id": "GMST/GMST_tmp.fnn"
                },
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                    "@id": "GMST/GeneMark_hmm.mod"
                },
                {
                    "@id": "GMST/seq_bin_2.mod"
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                {
                    "@id": "GMST/GMST_tmp"
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                {
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                },
                {
                    "@id": "GMST/seq_bin_1.mod"
                },
                {
                    "@id": "GMST/gms.log"
                },
                {
                    "@id": "GMST/GMST_tmp.faa"
                },
                {
                    "@id": "GMST/seq_bin_2"
                },
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                }
            ]
        },
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            "description": "SQANTI3 structural classification summary",
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            "contentSize": "2.5 KB",
            "sha256": "f4d5a27c8ecd088cecc13be6ca8f402042060fb396b55c8ad93d03a2271153a8"
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    ]
}