RiboSignal

Predicts a per-nucleotide ribosome P-site profile for a transcript from its sequence and matched RNA-seq coverage. It takes any transcript, coding or non-coding, up to 10,000 nt, the longest the checkpoints were trained on. No ribosome-profiling experiment is needed at inference.

The tutorial below runs the whole pipeline on public data, on chromosome 22, and ends with a number: predicted ORF calls scored against real Ribo-seq from the same donor. The Ribo-seq is there to score the prediction. The Nextflow pipeline takes RNA-seq alone, and the pack and predict pages show how to run the scripts without Ribo-seq.

Tutorial

• Install and check the environment
• Fetch and filter the annotation
• Get the sequencing data
• Measure the adapters before trimming
• Align and build coverage
• Build the pack and the ORF track
• Predict the profile
• Call ORFs
• Score against the real Ribo-seq
• Running it on a cluster
• Run it as a Nextflow pipeline