ADAR-SHAPE Pipeline Demo Data: Downsampled STK4 AluSq2 Sequencing FASTQs

Downsampled STK4 AluSq2 amplicon SHAPE/ADAR sequencing FASTQs serve as a demo dataset for the adar-shape-pipeline. The dataset includes reference sequences and primers, representing the full data to be deposited in GEO/SRA upon publication. Author Alain Laederach uploaded this dataset via the ODUM Harvested Dataverse platform.

Use Cases

• Benchmarking SHAPE-MaP data analysis pipelines based on the provided FASTQ files and reference sequences.
• Testing ADAR A-to-G read sorting and deconvolution algorithms mentioned in the pipeline description.
• Generating population-average RNA structure profiles using the ShapeMapper component referenced in the description.
• Validating normalization methods for sequencing data as part of the described pipeline workflow.

Strengths

• Contains approximately 300,000 read pairs per file, as stated in the description.
• Includes reference sequences and primers, providing necessary context for analysis.
• Serves as a representative demo for the full dataset, indicating curated relevance.

Limitations

• Row count and total dataset size are unknown, which may limit suitability assessment.
• Column-level documentation is absent; field semantics must be inferred after download.
• Description metadata is limited; actual data quality requires manual inspection after download.

Provenance

Source

ODUM Harvested Dataverse

Collection Method

Downsampled from STK4 AluSq2 amplicon SHAPE/ADAR sequencing.

Freshness

Last updated 2026-06-29 03:10:12; freshness should be verified.