The goal of this project is to compare DNA methylation between 3 methods: Whole Genome Bisulfite Sequencing (WGBS), Reduced Representation Bisulfite Sequencing (RRBS), and MethylBindingDomain Bisulfite Sequencing (MBDBS). To this end we have applied these 3 techniques to triplicate samples from two coral species, Montipora capitata and Pocillopora acuta (2 species x 3 methods x 3 samples = 18 libraries). Coral genomes are from the following resources Shumaker et al 2019 Scientific Reports https://www.nature.com/articles/s41598-019-39274-3 http://cyanophora.rutgers.edu/montipora/ http://cyanophora.rutgers.edu/montipora/Mcap.genome_assembly.fa.gz Vidal-Dupiol et al 2019 BioRxiv https://www.biorxiv.org/content/10.1101/698688v2 http://ihpe.univ-perp.fr/acces-aux-donnees/ http://ihpe.univ-perp.fr/telechargement/Data_to_downoload.rar --- Raw sequence data is available at NCBI at: As well as mirrored @ https://d.pr/cNbbta to download locally here is code snippet: ``` wget -r --no-directories --no-parent -P path/to/local/dir -A fastq.gz https://gannet.fish.washington.edu/seashell/bu-mox/data/froger/gannet.fish.washington.edu/tmp/00_fastq/ ``` --- Trimmed data is available at https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/ ``` wget -r --no-directories --no-parent -P path/to/local/dir -A fq.gz https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/ ``` --- BAM alignments are available at https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/ ``` wget -r --no-directories --no-parent -P path/to/local/dir -A .bam https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg/ wget -r --no-directories --no-parent -P path/to/local/dir -A .bam https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg/ ``` --- This project is funded by NSF 1756623 from BIOLOGICAL OCEANOGRAPHY, Integrtv Ecological Physiology, and EPSCoR