TagSeqTools

TagSeqTools identifies and analyzes NAD+-capped RNAs (NAD-RNAs) from NAD tagSeq data produced by Oxford Nanopore direct RNA sequencing to detect and quantify tagged RNA species.

Key Features:

• TagSeek module: Differentiates tagged and untagged reads within sequencing data to identify NAD-capped RNA molecules.
• TagSeqQuant module: Performs quantitative analysis of genes and isoforms from tagged and untagged read sets.
• RNA species detection: Detects isoforms, antisense transcripts, and pre-mRNA (un-spliced transcripts) from long-read data.
• Sequencing and labeling compatibility: Operates on NAD tagSeq data derived from chemo-enzymatic labeling and Oxford Nanopore direct RNA sequencing.
• Output generation: Produces plots and tables for visualization and downstream analysis.

Scientific Applications:

• NAD-RNA identification and quantification: Identification and quantification of NAD+-capped RNAs from NAD tagSeq experiments.
• Transcript isoform analysis: Characterization of transcript isoforms and un-spliced pre-mRNA using long-read direct RNA sequencing.
• Antisense transcript profiling: Detection and analysis of antisense transcripts in transcriptome-wide studies employing tagging-based methods.

Methodology:

The pipeline applies the TagSeek module to classify tagged versus untagged reads, uses TagSeqQuant for gene- and isoform-level quantification, includes modules to detect isoforms, antisense transcripts and pre-mRNA, and generates plots and tables as output.