how_are_we_stranded_here

how_are_we_stranded_here infers strandedness of paired-end RNA-Seq reads to provide strand-specificity information for quality control and downstream genomics and transcriptomics analyses.

Key Features:

• Strand-Specificity Assessment: Infers library orientation (forward or reverse) by evaluating the strand-specificity of paired-end RNA-Seq reads.
• Quality Control Integration: Reports strandedness metrics to inform RNA-Seq quality-control pipelines and decisions about downstream processing.
• Validation on Simulated and Real Reads: Demonstrated performance using both simulated and empirical RNA-Seq datasets to measure strandedness across data types.
• Contamination Indication: Flags datasets with strandedness outside expected ranges that may indicate sample contamination.

Scientific Applications:

• Genomics and Transcriptomics: Provides strand-specificity information required for accurate interpretation of RNA-Seq data in genomics and transcriptomics studies.
• Gene Expression and Differential Expression: Improves reliability of gene expression quantification and differential expression analyses by confirming library strandedness.
• RNA-Seq Quality Control: Detects strandedness issues and potential contamination during QC prior to downstream analyses.

Methodology:

Analyzes paired-end RNA-Seq reads and compares read alignments against known reference genomes or transcriptomes using algorithms to infer library orientation and compute strandedness metrics.