In preparation for some a bisulfite analysis requested by Steven, I needed to make bisulfite genome with, and for, Bismark to use and wanted to use the same one Yaamini has been working with. Downloaded the NCBI version of the C.virginica genome.
NCBI genome here:
SBATCH script contains all details regarding which genome was used as input and which software versions were used to produce the subsequent bisulfite genome:
#!/bin/bash ## Job Name #SBATCH --job-name=bismark ## Allocation Definition #SBATCH --account=coenv #SBATCH --partition=coenv ## Resources ## Nodes #SBATCH --nodes=1 ## Walltime (days-hours:minutes:seconds format) #SBATCH --time=10-00:00:00 ## Memory per node #SBATCH --mem=120G ##turn on e-mail notification #SBATCH --mail-type=ALL #SBATCH --mail-user=samwhite@uw.edu ## Specify the working directory for this job #SBATCH --workdir=/gscratch/scrubbed/samwhite/outputs/20190312_cvir_genome_prep_bismark # Load Python Mox module for Python module availability module load intel-python3_2017 # Document programs in PATH (primarily for program version ID) date >> system_path.log echo "" >> system_path.log echo "System PATH for $SLURM_JOB_ID" >> system_path.log echo "" >> system_path.log printf "%0.s-" {1..10} >> system_path.log echo ${PATH} | tr : \\n >> system_path.log # Directories and programs ## Programs bismark_dir="/gscratch/srlab/programs/Bismark-0.19.0" bowtie2_dir="/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64" samtools="/gscratch/srlab/programs/samtools-1.9/samtools" ## Files genome="/gscratch/srlab/sam/data/C_virginica/genomes/GCF_002022765.2_C_virginica-3.0/" # Prepare bisulfite genomes ${bismark_dir}/bismark_genome_preparation \ --path_to_bowtie ${bowtie2_dir} \ --verbose ${genome}
