strandCheckR

strandCheckR quantifies and removes putative double strand DNA contamination from strand-specific RNA samples.

Key Features:

• Contamination Quantification: strandCheckR calculates strandness information from BAM files to measure double strand DNA levels in strand-specific RNA data.
• Sliding Window Analysis: strandCheckR plots positive/negative proportions across all sliding windows to visualize contamination levels.
• Threshold-Guided Filtering: strandCheckR enables users to determine appropriate thresholds for filtering contaminated reads based on proportion plots.

Scientific Applications:

• RNA-seq Quality Control: strandCheckR assesses strand-specific RNA-seq libraries for double strand DNA contamination.
• Contamination Removal: strandCheckR filters putative double strand DNA reads from strand-specific RNA samples to improve downstream analyses.

Methodology:

strandCheckR calculates strandness information from BAM files and analyzes positive/negative proportions using sliding windows.