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IsoSeq Annotation (Map + Collapse + SQANTI3)

Sheep heart remote: pbmm2 + collapse + SQANTI3 (Oar_v3.1)

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Type
Custom
Status
succeeded
Engine
custom
Duration
0.2 h
Source Data
Study Tissue-specific IsoSeq transcriptome profiling of ovine cardiac ischemia model
Sample prep SMRTBell ligation of all sheep heart 17 cycle cDNA preps 2022-07-19
Sequencing Sequencing of sheep SMRTBell libraries on PacBio Sequel II at UQ 2022-08-08
Run Data Run #291 (6 samples)
Samples BORDER_cDNA_17_2kb_SMRTBell BORDER_cDNA_17_4kb_SMRTBell INFARCT_cDNA_17_2kb_SMRTBell INFARCT_cDNA_17_4kb_SMRTBell REMOTE_cDNA_17_2kb_SMRTBell REMOTE_cDNA_17_4kb_SMRTBell
Pipeline
IsoSeq Clustering (Refine + Cluster)
Run #68
succeeded
IsoSeq Annotation (Map + Collapse + SQANTI3)
Run #71 (this run)
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
26,728
Genes
24,746
FSM
789
ISM
1,360
NIC
495
NNC
1,588
Canonical SJ
16.0%

SQANTI3 Structural Categories

SQANTI3 Subcategories

Full-Length Read Support per Isoform

26,728 isoforms | Median FL: 1 | Mean FL: 1.4 | Max FL: 65

Transcript Length Distribution

26,728 transcripts | Median: 2,818 nt | Mean: 2,698 nt | N50: 3,446 nt

Exons per Transcript

Output Files

GMST
FileSize
GMST_tmp HPC 5.8 MB
GMST_tmp.faa HPC 2.4 MB
GMST_tmp.fnn HPC 6.2 MB
GeneMark_hmm.mod HPC 190.6 KB
gms.log HPC 16.8 KB
seq_bin_1 HPC 26.5 MB
seq_bin_1.mod HPC 63.4 KB
seq_bin_2 HPC 22.7 MB
seq_bin_2.mod HPC 63.4 KB
seq_bin_3 HPC 20.2 MB
seq_bin_3.mod HPC 63.4 KB
RTS
FileSize
sj.rts.results.tsv HPC 379.7 KB
Root
FileSize
collapsed.abundance.txt HPC 459.9 KB
collapsed.fasta HPC 70.5 MB
collapsed.flnc_count.txt HPC 329 KB
collapsed.gff HPC 6.8 MB
collapsed.group.txt HPC 879.2 KB
collapsed.read_stat.txt HPC 5.5 MB
collapsed.report.json HPC 704 B
mapped.bam HPC 33.9 MB
mapped.bam.bai HPC 1.7 MB
refAnnotation_sheep_heart_remote.genePred HPC 7.3 MB
results_summary.json HPC 2.4 KB
sheep_heart_remote.params.txt HPC 826 B
sheep_heart_remote_SQANTI3_report.html HPC 7.4 MB
sheep_heart_remote_classification.txt HPC 7.6 MB
sheep_heart_remote_corrected.faa HPC 2.2 MB
sheep_heart_remote_corrected.fasta HPC 70.1 MB
sheep_heart_remote_corrected.genePred HPC 3.1 MB
sheep_heart_remote_corrected.gtf HPC 6.8 MB
sheep_heart_remote_corrected.gtf.cds.gff HPC 10 MB
sheep_heart_remote_junctions.txt HPC 3.2 MB
unknown_strand.gtf HPC 0 B

Provenance

Execution IsoSeq Annotation: pbmm2 + collapse + SQANTI3 (sheep_heart_remote, Ovis aries Oar_v3.1)
Started 2026-03-04T12:45:00+00:00
Completed 2026-03-04T02:56:12+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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            "name": "IsoSeq Annotation (sheep_heart_remote, Ovis aries Oar_v3.1) \u2014 Run #71",
            "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": "sheep_heart_remote_junctions.txt"
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                {
                    "@id": "sheep_heart_remote_corrected.genePred"
                },
                {
                    "@id": "sheep_heart_remote_corrected.fasta"
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                    "@id": "sheep_heart_remote_SQANTI3_report.html"
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                    "@id": "sheep_heart_remote_corrected.gtf"
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                    "@id": "unknown_strand.gtf"
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                {
                    "@id": "mapped.bam.bai"
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                {
                    "@id": "sheep_heart_remote.params.txt"
                },
                {
                    "@id": "sheep_heart_remote_classification.txt"
                },
                {
                    "@id": "sheep_heart_remote_corrected.gtf.cds.gff"
                },
                {
                    "@id": "collapsed.report.json"
                },
                {
                    "@id": "collapsed.abundance.txt"
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                    "@id": "mapped.bam"
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                    "@id": "refAnnotation_sheep_heart_remote.genePred"
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                    "@id": "GMST/GMST_tmp.faa"
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                    "@id": "GMST/seq_bin_2"
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        },
        {
            "@id": "#isoseq",
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            "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",
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        {
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            "name": "sheep_heart_remote_junctions.txt",
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            "sha256": "60aa2bda9b71823d31c221d313b872145d5357e48d5892bfc130180370b15bb0"
        },
        {
            "@id": "sheep_heart_remote_corrected.genePred",
            "@type": "File",
            "name": "sheep_heart_remote_corrected.genePred",
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            "contentSize": "3.1 MB",
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        },
        {
            "@id": "sheep_heart_remote_SQANTI3_report.html",
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            "name": "sheep_heart_remote_SQANTI3_report.html",
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            "contentSize": "7.4 MB",
            "sha256": "de2d10c471c56fdd6b2483be420705cc0f40276cebf7ede4f3442dc9c6d12321"
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        {
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            "name": "sheep_heart_remote_corrected.gtf",
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            "sha256": "5415c4d523f8d873783649810ca5b108551e8eb00ea6a9266b7a784496515d43"
        },
        {
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        {
            "@id": "sheep_heart_remote.params.txt",
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            "sha256": "29a5f40922a84714d2fdb3a71ca87263421db9a4249b1917fd5be7f51bd360e7"
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        {
            "@id": "sheep_heart_remote_classification.txt",
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        {
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        {
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            "@type": "CreateAction",
            "name": "IsoSeq Annotation: pbmm2 + collapse + SQANTI3 (sheep_heart_remote, Ovis aries Oar_v3.1)",
            "instrument": {
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            },
            "startTime": "2026-03-04T12:45:00+00:00",
            "endTime": "2026-03-04T02:56:12+00:00",
            "result": [
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                {
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                {
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                {
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                {
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                },
                {
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                {
                    "@id": "refAnnotation_sheep_heart_remote.genePred"
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                {
                    "@id": "sheep_heart_remote_corrected.faa"
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                {
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                {
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                },
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                },
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                }
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    ]
}