Current status of e5 3 species lncRNA comparative work from SICB slides
Next steps
Currently at a stage where we are comfortable with resulting lncRNAs. Next steps:
- Location with BEDtools
- Pull transcript IDs hits between species
- Pull hits for hits between species and reference RNAcentral ID to get actual annotation
- Lit review for conserved region analysis
- Develop or find pipeline for comparing lncRNAs to known conserved regions across many species
- Develop or find pipeline for comparing sequences and finding conserved regions as opposed to full sequence similarity between 3 species
- Run conserved region analysis for similarity to known conserved regions
- Run conserved region analysis to identify conserved regions between the 3 coral species
- Expression histograms for lncRNAs in each species
- lncRNA WGCNA runs
- mRNA WGCNA runs
- Correlations between lncRNA and mRNA modules in each species
- Comparisons in expression patterns between species?