Differential DNA methylation and RNAseq analyses
- RSEM for mapping to transcriptome
- EdgeR for transcript count normalization, differential expression analyses and plotting heat maps
- nf-core Methylseq for WGBS mapping and calling methylated C's
- Run on wild, phenology, and seedling data
- Metilene and Methylkit for detecting DMRs
- Run for detecting various Wild, Seedling, and Phenology DMRS
- Scripts for preparing files for Metilene and running metilene
- Bedtools for comparisons
- Crosses over DMRs, to find intersecting or non-intersecting DMRS
- Script for extending DMRS, and mapping to fasta file
- Notes on Blasting DMRS to reference and to NCBI
- Scripts for running interproscan on a set of files
- Script on running interproscan on divided subseq files
- Script for formatting file to run on interproscan
- Notes on running interproscan on both Methylation and RNA data, and on comparing/combining the two
- ErmineJ for GO term enrichment
- Several scripts for plotting
- General notes on heatmap plotting (RNA and methylation)
- Notes on inheritence plotting
- BS-SNP for SNP calling from bisulphite treated DNA
- Basic popgen analyses
- Comparing phenotypes and traits of the warmed and control plants
- Notes on original runs of certain anlyses + analyses not yet used/completed
- Phenogram script for interproscan + annotation file to format to phenogram
- gff3 to cds conversion