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 forSTAR
,salmon
,riboprof
, andriboss.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.