This repository hosts analyses and datasets from Ashey et al. 2025, which examines ncRNAs in three coral species.
Citation: Ashey J, Rodriguez Casariego J, Bengtsson Z, Huffmyer AS, Becker DM, Durkin KM, White S, Eirin-Lopez J, Putnam HM, Roberts SB. 2025. Non-coding RNA Repertoire in reef-building corals. bioRxiv. https://doi.org/10.1101/2025.03.15.643469.
- DIVE genome browser - View ncRNA features across all three species in our interactive genome browser.
- OSF Project Link - Access large genomic reference files in our Open Science Framework (OSF) storage directory.
- Access raw RNA sequences stored on NCBI.
- Access raw small RNA sequences stored on NCBI.
Top level directories are organized by species.
For instance:
A-Pver
B-Mcap
C-Pacu
D-Apul
E-Peve
F-Ptua
Each species folder contains 3 directories:
data # raw and processed data files
code # Analysis code (prefix files with two digit number, eg 01-*.Rmd)
output # organized into subfolders matching two digit code names
Example: Output for 01-methylation-explore.Rmd is stored in A-Pver/output/01-methylation-explore/.
Please use Relative Paths. Commit and Push often.
The table below provides links to lncRNA, miRNA, and piRNA feature and fasta files for the three species.
| Species | miRNA FASTA | miRNA GFF3 | piRNA BED | lncRNA BED | lncRNA FASTA |
|---|---|---|---|---|---|
| Apul | mir.fasta | Results.gff3 | piRNA clusters | lncRNA.bed | lncRNA.fasta |
| Peve | mir.fasta | Results.gff3 | piRNA clusters | lncRNA.bed | lncRNA.fasta |
| Ptuh | mir.fasta | Results.gff3 | piRNA clusters | lncRNA.bed | lncRNA.fasta |
See our species descriptions and genomic resources wiki page for more details on reference genomes and annotation sources.