gannet/Atumefaciens/20181015_oly_WGBSseq_v081

This directory contains the results of Bismark methylation analysis on Olympia oyster, whole genome bisulfite sequencing data.

Used default Bowtie2 settings.

Trimmed (TrimGalore!, 10bp 5') FastQ files from 20180830 were used as input.

Trimming notebook entry:

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Bismark was run on Mox. See the SLURM file 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:

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FILES (non-Bismark)

- 20181015_oly_WGBSseq_v081.sh: Mox SBATCH script for Bismark pipeline.

- slurm-375266.out: Mox output log.

- system_path.log: A text file attempting to document various program versions being used by Mox.