IsoQuant Publication Data: Mouse RNA-Seq Simulated and SIRV Benchmarking Data

30 million reads of simulated mouse ONT R10.4 data with a 2.8% error rate, alongside SIRV Set4 sequencing data, were used to benchmark the IsoQuant tool. The dataset includes multiple simulated and experimental RNA-seq files mapped to the GRCm39 genome or SIRV reference, created by Andrey D. Prjibelski. It also contains a reduced mouse GENCODE vM26 annotation with 15% of expressed isoforms removed.

Use Cases

• Benchmarking isoform quantification tools based on simulated mouse PacBio and ONT reads with defined error rates.
• Evaluating sequencing platform performance based on SIRV (Spike-In RNA Variants) control data sequenced with ONT R9.4 chemistry.
• Training machine learning models for transcriptome assembly using the provided reduced mouse annotation with expressed transcripts.
• Assessing mapping accuracy and error profiles based on reads aligned to the GRCm39 genome using minimap2.

Strengths

• Includes 30 million reads of simulated ONT R10.4 data with a specified 2.8% error rate.
• Provides a reduced mouse annotation where 15% of expressed isoforms were removed, based on real mouse brain sequencing data.
• Contains multiple data types: simulated PacBio (6 million reads), ONT R9.4/R10.4, and experimental SIRV data for comparative analysis.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Last update date is unknown; freshness unverified.
• A noted discrepancy exists where a file named for R10.4 data actually contains R9.4 data.

Provenance

Source

University of Helsinki

Collection Method

Data was generated via simulation (IsoSeqSim, NanoSim) and experimental sequencing (ONT MinION) for the IsoQuant publication.