Tutorials

• Run the ORF discovery pipeline
• How to use existing alignment files
• How to use the containers

The tutorials includes a small test Ribo-seq dataset and reference Rp-Bp output that is also used for regression tests. It has been constructed to include some reads which uniquely map to the annotated transcripts, some reads which map to ribosomal sequences, some reads which do not uniquely map to the genome, and some reads which are filtered due to quality issues.

Download the dataset

Click here and unzip the archive. Navigate to the c-elegans-chrI-example directory.

Content

• c-elegans-test.yaml The YAML configuration file.

• c-elegans.alignments-only.yaml Another YAML configuration to explain How to use existing alignment files.

input

• c-elegans.test-chrI.rep-1.fastq.gz Ribo-seq sample 1.

• c-elegans.test-chrI.rep-2.fastq.gz Ribo-seq sample 2.

• WBcel235.chrI.fa The reference sequence of Chromosome I for C. elegans.

• WBcel235.79.chrI.gtf The Ensembl, version 79 annotation, for Chromosome I for C. elegans.

• X03680_1.fasta The sequence of the ribosomal subunits for C. elegans. The reference accession is X03680.1.

• riboseq-adapters.fa An example adapter file. It includes typical TruSeq and ArtSeq adapters, as well as a few adapters from the literature. It also includes a custom adapter used to create the sample dataset.

reference

This directory contains reference genome annotations and predictions generated by Rp-Bp.