FixSEQ

FixSEQ corrects over-dispersion in per-base read count distributions from high-throughput sequencing datasets such as RNA-seq, DNase-seq, and ChIP-seq to improve the accuracy of downstream analyses.

Key Features:

• Nonparametric Approach: Employs a nonparametric method that does not rely on Poisson or negative binomial distributional assumptions.
• Universal Application: Applies across sequencing techniques including RNA-seq, DNase-seq, and ChIP-seq without distribution-specific tuning.
• Over-Dispersion Correction: Adjusts per-base read count distributions to account for over-dispersion and normalize data for downstream analysis.

Scientific Applications:

• Differential Expression Analysis: Improves identification of differentially expressed genes by providing corrected per-base read counts.
• Transcription Factor Binding Site Mapping: Enhances detection of transcription factor binding sites from ChIP-seq data through over-dispersion correction.
• Chromatin Accessibility Profiling: Refines identification of chromatin accessibility regions from DNase-seq by normalizing per-base read counts.

Methodology:

Performs a systematic, nonparametric adjustment of per-base read counts to correct over-dispersion without imposing Poisson or negative binomial parametric models.