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This workflow analyses Oxford Nanopore long-read RNA sequencing data. It uses
bambu to build and quantify
transcript models, can optionally run
SQANTI3 for transcript classification
and QC, and can optionally run
DESeq2 and
DEXSeq for differential
analysis.
The workflow supports:
- transcript identification from either cDNA or direct RNA reads
- transcript discovery guided by a supplied genome and annotation
- quantification against a supplied reference annotation
- optional transcript classification and QC with
SQANTI3 - differential gene expression with
DESeq2 - differential transcript usage with
DEXSeq
The main transcriptome result is a shared bambu model built from all samples
together. The workflow also produces separate per-sample transcriptomes, so
each sample has its own GTF, FASTA, count tables, and optional SQANTI3
summary alongside the shared results.
For users familiar with earlier transcriptome workflows, the main change is
that transcript discovery, quantification, and optional differential analysis
now use the shared bambu outputs rather than the older
StringTie/GffCompare/Salmon-based approach. The rest of this README explains
the current workflow in plain terms, while the FAQ and Troubleshooting
sections call out the main differences from the previous workflow version.