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IsoSeq Annotation (Map + Collapse + SQANTI3)

Annotation: DBA 2017 combined (I-K2 + K7-50pM)

Download ZIP JSON-LD
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
Run #77
succeeded
IsoSeq Clustering (Refine + Cluster)
Run #87
succeeded 2 sources
IsoSeq Annotation (Map + Collapse + SQANTI3)
Run #97 (this run)
succeeded 1 sources
Functional Annotation (TransDecoder + Pfam + SwissProt)
Run #107
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
14,697
Genes
8,053
FSM
9,284
ISM
1,518
NIC
1,572
NNC
2,014
Canonical SJ
86.6%

SQANTI3 Structural Categories

SQANTI3 Subcategories

Full-Length Read Support per Isoform

14,697 isoforms | Median FL: 1 | Mean FL: 1.7 | Max FL: 40

Transcript Length Distribution

14,697 transcripts | Median: 2,595 nt | Mean: 2,770 nt | N50: 3,235 nt

Exons per Transcript

Output Files

GMST
FileSize
GMST_tmp HPC 3.8 MB
GMST_tmp.faa HPC 7.5 MB
GMST_tmp.fnn HPC 21 MB
GeneMark_hmm.mod HPC 190.6 KB
gms.log HPC 17.8 KB
seq_bin_1 HPC 14.3 MB
seq_bin_1.mod HPC 63.4 KB
seq_bin_2 HPC 12.6 MB
seq_bin_2.mod HPC 63.4 KB
seq_bin_3 HPC 12.2 MB
seq_bin_3.mod HPC 63.4 KB
RTS
FileSize
sj.rts.results.tsv HPC 257.2 KB
Root
FileSize
collapsed.abundance.txt HPC 246.5 KB
collapsed.fasta HPC 39.7 MB
collapsed.flnc_count.txt HPC 174.3 KB
collapsed.gff HPC 14.1 MB
collapsed.group.txt HPC 534.7 KB
collapsed.read_stat.txt HPC 7.7 MB
collapsed.report.json HPC 703 B
mapped.bam HPC 15.8 MB
mapped.bam.bai HPC 1.3 MB
mouse_dba_2017.params.txt HPC 815 B
mouse_dba_2017_SQANTI3_report.html HPC 6.5 MB
mouse_dba_2017_classification.txt HPC 10.4 MB
mouse_dba_2017_corrected.faa HPC 7.2 MB
mouse_dba_2017_corrected.fasta HPC 39.5 MB
mouse_dba_2017_corrected.genePred HPC 4.3 MB
mouse_dba_2017_corrected.gtf HPC 14.1 MB
mouse_dba_2017_corrected.gtf.cds.gff HPC 29.6 MB
mouse_dba_2017_junctions.txt HPC 15.9 MB
refAnnotation_mouse_dba_2017.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_2017, Mus musculus GRCm39)
Started 2026-03-05T09:40:11+00:00
Completed 2026-03-04T23:46:39+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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            "datePublished": "2026-03-04",
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                    "@id": "mouse_dba_2017_corrected.gtf"
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                    "@id": "mapped.bam"
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                {
                    "@id": "mouse_dba_2017_junctions.txt"
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                    "@id": "mouse_dba_2017_classification.txt"
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                {
                    "@id": "GMST/seq_bin_2"
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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_dba_2017, Mus musculus GRCm39)",
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            "startTime": "2026-03-05T09:40:11+00:00",
            "endTime": "2026-03-04T23:46:39+00:00",
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    ]
}