Comparison of the ability of open reading frames to recruit ribosomes within individual transcripts.

Dependencies:

• snakemake=5.24.0
• STAR=2.7.5c (https://github.com/alexdobin/STAR)
• salmon=1.3.0 (https://github.com/COMBINE-lab/salmon)
• riboprof=1.2 (https://github.com/Kingsford-Group/ribomap)
• Biopython=1.77
• pysam=0.15.3
• pandas=1.1.1
• scipy=1.5.2
• matplotlib=3.3.1
• seaborn=0.10.1

riboprof is available as a precompiled executable. Other dependencies can be installed through conda or pip.

The python scripts can be executed independently.

• prep_reference_files.py prepares the reference transcriptome files for STAR, salmon, riboprof, and riboss.py.
• select_footprint_size.py selects the best ribosome footprint sizes by triplet periodicity using Fisher's exact test.
• riboss.py compares the strength of upstream and downstream ORFs with main ORFs using Fisher's exact test.

Snakemake is only required to run the example pipeline as follows:

snakemake -j1 -s riboss.smk

Related article:

• Lim, C.S., Wardell, S.J.T., Kleffmann, T. & Brown, C.M. (2018) The exon-intron gene structure upstream of the initiation codon predicts translation efficiency. Nucleic Acids Res. 46: 4575-4591.