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IsoSeq Annotation (Map + Collapse + SQANTI3)

Annotation: DBA I-K2 (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 #75
succeeded
IsoSeq Clustering (Refine + Cluster)
Run #80
succeeded 1 sources
IsoSeq Annotation (Map + Collapse + SQANTI3)
Run #90 (this run)
succeeded 1 sources
Functional Annotation (TransDecoder + Pfam + SwissProt)
Run #100
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
7,460
Genes
5,098
FSM
5,265
ISM
572
NIC
631
NNC
884
Canonical SJ
88.4%

SQANTI3 Structural Categories

SQANTI3 Subcategories

Full-Length Read Support per Isoform

7,460 isoforms | Median FL: 1 | Mean FL: 1.4 | Max FL: 19

Transcript Length Distribution

7,460 transcripts | Median: 2,630 nt | Mean: 2,774 nt | N50: 3,249 nt

Exons per Transcript

Output Files

GMST
FileSize
GMST_tmp HPC 2 MB
GMST_tmp.faa HPC 3.9 MB
GMST_tmp.fnn HPC 10.9 MB
GeneMark_hmm.mod HPC 190.6 KB
gms.log HPC 15.7 KB
seq_bin_1 HPC 6.9 MB
seq_bin_1.mod HPC 63.4 KB
seq_bin_2 HPC 6.4 MB
seq_bin_2.mod HPC 63.4 KB
seq_bin_3 HPC 6.5 MB
seq_bin_3.mod HPC 63.4 KB
RTS
FileSize
sj.rts.results.tsv HPC 132.4 KB
Root
FileSize
collapsed.abundance.txt HPC 123.9 KB
collapsed.fasta HPC 20.2 MB
collapsed.flnc_count.txt HPC 87.2 KB
collapsed.gff HPC 7.3 MB
collapsed.group.txt HPC 229.3 KB
collapsed.read_stat.txt HPC 2.6 MB
collapsed.report.json HPC 702 B
mapped.bam HPC 7.6 MB
mapped.bam.bai HPC 1.3 MB
mouse_dba_i_k2.params.txt HPC 815 B
mouse_dba_i_k2_SQANTI3_report.html HPC 5.8 MB
mouse_dba_i_k2_classification.txt HPC 5.4 MB
mouse_dba_i_k2_corrected.faa HPC 3.7 MB
mouse_dba_i_k2_corrected.fasta HPC 20.1 MB
mouse_dba_i_k2_corrected.genePred HPC 2.2 MB
mouse_dba_i_k2_corrected.gtf HPC 7.3 MB
mouse_dba_i_k2_corrected.gtf.cds.gff HPC 15.5 MB
mouse_dba_i_k2_junctions.txt HPC 8.3 MB
refAnnotation_mouse_dba_i_k2.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_i_k2, Mus musculus GRCm39)
Started 2026-03-05T09:04:56+00:00
Completed 2026-03-04T23:12:02+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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            "description": "IsoSeq post-clustering annotation: pbmm2 + isoseq collapse + SQANTI3",
            "datePublished": "2026-03-04",
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                    "@id": "mouse_dba_i_k2_junctions.txt"
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                    "@id": "mouse_dba_i_k2_SQANTI3_report.html"
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        {
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        {
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        {
            "@id": "#execution",
            "@type": "CreateAction",
            "name": "IsoSeq Annotation: pbmm2 + collapse + SQANTI3 (mouse_dba_i_k2, Mus musculus GRCm39)",
            "instrument": {
                "@id": "#pbmm2"
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            "startTime": "2026-03-05T09:04:56+00:00",
            "endTime": "2026-03-04T23:12:02+00:00",
            "result": [
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                {
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                {
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                {
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                },
                {
                    "@id": "mouse_dba_i_k2_SQANTI3_report.html"
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                {
                    "@id": "mapped.bam"
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                {
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                {
                    "@id": "mouse_dba_i_k2_corrected.gtf.cds.gff"
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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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            "@type": "File",
            "name": "results_summary.json",
            "description": "SQANTI3 structural classification summary",
            "encodingFormat": "application/json",
            "contentSize": "2.4 KB",
            "sha256": "e7be61490a925da5049d6026a9b19daa041185557bb84af877f656a4c163004c"
        }
    ]
}