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Functional Annotation (TransDecoder + Pfam + SwissProt)

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

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Type
Custom
Status
succeeded
Engine
custom
Duration
1.8 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
succeeded 1 sources
Functional Annotation (TransDecoder + Pfam + SwissProt)
Run #105 (this run)
succeeded 1 sources
Combined From

Software Tools

ToolVersionURL
TransDecoder - https://github.com/TransDecoder/TransDecoder
HMMER (hmmscan) - http://hmmer.org/
diamond - https://github.com/bbuchfink/diamond
Singularity - https://sylabs.io/singularity/

Results Summary

Transcripts
20,186
Pfam Coverage
82.1%
SwissProt Coverage
88.0%
Domain Variant Genes
667

Peptide Length Distribution

18,564 ORFs | Median: 423 aa | Mean: 496 aa | Max: 2,912 aa

Evidence Tier Distribution

Frame Impact Classification

Top Pfam Domains

ORF Type Distribution

Output Files

blastp.tsv HPC 2.9 MB gene_functional_summary.tsv HPC 578.9 KB isoform_annotations.tsv HPC 3.9 MB mouse_dba_combined_corrected.fasta.transdecoder.bed HPC 2.1 MB mouse_dba_combined_corrected.fasta.transdecoder.cds HPC 28.8 MB mouse_dba_combined_corrected.fasta.transdecoder.gff3 HPC 10.4 MB mouse_dba_combined_corrected.fasta.transdecoder.pep HPC 10.9 MB pfam.domtblout HPC 11.7 MB rep_besthit.tsv HPC 2.5 MB rep_pfam.tsv HPC 460.1 KB results_summary.json HPC 2.5 KB

Provenance

Execution IsoSeq Functional Annotation: TransDecoder + Pfam + SwissProt (mouse_dba_combined)
Started 2026-03-06T09:44:10+00:00
Completed 2026-03-06T01:29:04+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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}