owl/Athaliana/20180913_oly_WBGSseq_bismark This directory contains the results of Bismark methylation analysis on Olympia oyster, whole genome bisulfite sequencing data. Used a more relaxed bowtie2 score setting than default: --score_min L,0,-0.6 Trimmed (TrimGalore!, 10bp 5') FastQ files from 20180830 were used as input. Trimming notebook entry: - Bismark was run on Mox. See the two SLURM files for info on how the job was run. Data has been deduplicated, sorted, and indexed, so it's ready for downstream analysis in MethylKit (R package) and IGV. Data set info is here: - https://github.com/RobertsLab/project-olympia.oyster-genomic/wiki Notebook entry: - ------------------- FILES (non-Bismark) - 20180912_oly_WGBSseq_bismark.sh: Mox SBATCH script for Bismark pipeline. Contains a typo in the sort portion of the pipeline. Sort was run independently (see sort.sh). - slurm-301955.out: Mox output log from initial Bismark run. - slurm-302791.out: Mox output log from sort step in Bismark run. Fixed typo in original SBATCH submission script. - sort.sh: Mox SBATCH submission script for sort portion of Bismark pipeline. Resolves typo in original SBATCH submission script. - system_path.log: A text file attempting to document various program versions being used by Mox.