Petrisnake: Benchmark Outputs for Bacterial Single-Cell RNA-Seq Pipelines

Output data files from a benchmarking study comparing two bioinformatic pipelines for bacterial single-cell RNA-seq. The data includes gene count matrices and UMI count tables generated by the original PETRI-seq pipeline and the new Petrisnake pipeline, based on a sample of exponential phase Escherichia coli cells. The dataset was authored by Jakob Peder Pettersen and last updated on 2026-04-21.

Use Cases

• Benchmarking computational pipelines for bacterial single-cell RNA-seq based on the provided gene count matrices.
• Reproducing the comparative analysis figure from the associated paper based on the included R script and output data.
• Evaluating UMI counting performance in single-cell bacterial data based on the provided UMI count tables.

Strengths

• Includes output data from two distinct bioinformatics pipelines for direct comparison.
• Contains an R script to regenerate the primary comparative figure from the associated paper.
• Last updated on 2026-04-21, indicating recent maintenance.

Limitations

• Row count and file size are unknown, which may limit suitability assessment.
• Column-level documentation is absent; field semantics must be inferred after download.
• The raw sequence data is not included and must be downloaded separately from NCBI (SRR28148450).

Provenance

Source

DataverseNO Harvested Dataverse

Collection Method

Generated as output from bioinformatics pipelines (PETRI-seq and Petrisnake).

Time Range

Based on data from a 2024 study (Yan et al. 2024).

Freshness

Last updated 2026-04-21 02:26:35

Geography

null