txcutr

txcutr implements convenience methods for generating truncated transcriptome annotations and their corresponding sequences to aid isoform usage quantification from end-specific mRNA sequencing data.

Key Features:

• Truncated annotation generation: Produces truncated versions of transcriptome annotations for use in alignment or pseudo-alignment and downstream analysis.
• Sequence generation: Generates sequences corresponding to the truncated transcriptome annotations.

Scientific Applications:

• Isoform usage quantification: Supports analyses focusing on quantification of isoform usage from mRNA sequencing data generated by library preparation methods that produce reads from transcript ends.
• Alignment optimization: Enables use of truncated annotations at the alignment or pseudo-alignment stage for end-specific sequencing data.

Methodology:

The package implements convenience methods for generating truncated transcriptome annotations and their corresponding sequences.