README file for intermediate data files associated with project "Evolution of DNA methylation across arthropods"

"all_species_genes.csv" = summary file of exon methylation level and other characteristics for each gene in each species, generated using the script "gene_preprocessing.R" (https://github.com/SamuelHLewis/arthropod-dna-methylation)

"all_species_TEs.csv" = summary file of methylation level and other characteristics for each TE in each species, generated using the script "TE_preprocessing.R" (https://github.com/SamuelHLewis/arthropod-dna-methylation)

all files with the suffix ".gff" = annotation files for each genome, generated using the scripts "gene_exon_CDS_renamer.py", "spliceform_CDS_exon_merger.py", "GFF_splitter.py" and "UTR_intron_flank_finder.py" from GFFtoolkit (https://github.com/SamuelHLewis/GFFtoolkit)

all files with the suffix "_CpG_annotated.txt" = summary file of methylation level and other characteristics for each CpG with >=10x coverage on both strands in each species, generated using the script "CpG_annotator.py" from BStoolkit (https://github.com/SamuelHLewis/BStoolkit)

all files with the suffix "_FPKM.csv" = expression levels (in FPKM) for each gene in each species, generated using bowtie-2 and DESeq2

"Concatenated.MAFFT.Gblocks.MCC.nex" = time-scaled phylogenetic tree for focal species, generated using BEAST

"Dmel_genes_orthogroups.csv" = D. melanogaster gene names and the orthogroups that they belong to, generated using orthofinder

"DNMT_ALKB2_gene_counts.csv" = Counts of DNMT and ALKB2 genes in each species

"exon_methylation_ancestral.nex" = nexus file containing the maximum likelihood estimates of exon methylation at each internal node of the focal species tree

"exon_TE_upstream_methylation_mean_CI.csv" = mean methylation levels and their 95% confidence intervals for exons, upstream regions, TEs and unannotated CpGs in each species

"exon_tip_states.txt" = mean exon methylation level for each species

"genome_wide_methylation_ancestral.nex" = nexus file containing the maximum likelihood estimates of genome-wide methylation at each internal node of the extended species tree (focal species and previous studies)

"genome_wide_tip_states.txt" = mean genome-wide methylation level of each species in the extended species tree (focal species and previous studies)

"previous_studies_methylation.csv" = mean genome-wide methylation level estimates from previous studies, including citations to previous studies

"spike_in.csv" = percentage of reads mapping to the unmethylated spike-in in each library from each biological replicate, which gives an estimate of the bisulphite conversion efficiency

"TE_methylation_ancestral.nex" = nexus file containing the maximum likelihood estimates of TE methylation at each internal node of the focal species tree

"TE_tip_states.txt" = mean TE methylation level for each species

"timetree_species_renamed_lengthadj.nwk" = time-scaled phylogenetic tree for the extended set of species (focal species and previous studies), obtained from www.timetree.org