qtlseq-refine
Overview
qtlseq-refine is a Python-based analysis repository for refining QTL-seq signals using high-resolution, multi-scale sliding-window analysis of significant ΔSNP-index regions.
Purpose
It was developed to improve the mapping resolution of conventional QTL-seq analysis, which often relies on large sliding windows for genome-wide SNP-index estimation. The workflow focuses on re-analyzing significant ΔSNP-index signals with smaller window scales to refine candidate genomic intervals.
Key features
- Multi-scale sliding-window analysis of p99-filtered ΔSNP-index data
- Empirical QTL-seq re-analysis using OsABCI8 and OsLESV datasets
- Monte Carlo simulation for validating p99 filtering threshold
- Simulation-based assessment of positional bias caused by window assignment convention
- Excel-based input and output files for practical downstream analysis and visualization
GitHub
Current status
Available as a public manuscript-associated repository providing Python scripts, example datasets, and simulation workflows for high-resolution refinement of QTL-seq ΔSNP-index signals.