Tutorials

The tutorials include a small test Ribo- and RNA-seq dataset and reference 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 hiPSC-CM-chr1-example directory.

Content

  • hiPSC-CM-test.yaml The YAML configuration file.

input

  • ribo-ORFs.chr1.gtf The Rp-Bp Ribo-seq ORF predictions for chromosome 1.

  • ribo-adapters.fa An example adapter file for this dataset (Ribo-seq).

  • rna-adapters.fa An example adapter file for this dataset (RNA-seq).

  • GRCh38.102.chr1 The annotation directory with the Bowtie 2 and STAR indices, the Ensembl GTF for chromosome 1, and the corresponding transcripts in BED12+ format.

  • hiPSC-CM.ribo.test-chr1.rep-d01-1.fastq.gz Ribo-seq sample 1.

  • hiPSC-CM.ribo.test-chr1.rep-d01-2.fastq.gz Ribo-seq sample 2.

  • hiPSC-CM.ribo.test-chr1.rep-d05-1.fastq.gz Ribo-seq sample 3.

  • hiPSC-CM.ribo.test-chr1.rep-d05-2.fastq.gz Ribo-seq sample 4.

  • hiPSC-CM.rna.test-chr1.rep-d01-1.fastq.gz RNA-seq sample 1.

  • hiPSC-CM.rna.test-chr1.rep-d01-2.fastq.gz RNA-seq sample 2.

  • hiPSC-CM.rna.test-chr1.rep-d05-1.fastq.gz RNA-seq sample 3.

  • hiPSC-CM.rna.test-chr1.rep-d05-2.fastq.gz RNA-seq sample 4.

reference

This directory contains the final output generated by Ribotools for abundance estimation (count tables for Ribo- and RNA-seq, periodicity estimates for Ribo-seq), and TEA (sample table and output for the LRT model).