TSSi

TSSi identifies and normalizes transcription start sites (TSSs) in 5' mRNA tag high-throughput sequencing data as an R package.

Key Features:

• Heuristic framework: Employs a heuristic probabilistic framework to model the distribution of mapped reads and account for mapping imprecision relative to true TSS positions.
• User-adaptable assumptions: Allows adjustment of probabilistic assumptions about observed read positions and systematic mapping errors to match dataset-specific characteristics.
• Regularization procedure: Applies a preprocessing regularization step to reduce noise and decrease false positives in TSS identification from 5' mRNA tag data.

Scientific Applications:

• Gene Expression Studies: Pinpoints exact TSS locations to support analysis of transcriptional regulation in RNA-seq datasets.
• Transcription Factor Binding Analysis: Maps TSSs to investigate transcription factor interactions using ChIP-seq and related assays.
• Epigenetic Research: Enables exploration of chromatin states and DNA modifications near TSSs that influence transcription initiation.

Methodology:

Analyzes 5' mRNA tag data by modeling observed mapped read positions and potential systematic mapping errors with a heuristic probabilistic model and applies a regularization step to reduce noise.