Sam’s Notebook: Data Management – Create C.virginica Bisulfite Genome with Bismark on Mox

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:

https://ift.tt/2VVM8YO

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} 

Sam’s Notebook: MBD Enrichment – Ethanol Precipitation of C.virginica MBD samples

After completing two rounds of MBD enrichment (first 12 samples on 20190307 and the second 12 samples on 20190311), I performed ethanol precipitation, per the MethylMiner instructions with the following modifications:

  • after additions of glycogen, sodium acetate and ethanol, incubated samples O/N at -80oC
  • spins were performed at 13,000g

Samples were resuspended in 25uL of PCR H2O.

Currently, don’t have appropriate tubes for quantification, so will do so once they arrive.

Samples were stored in the small -20oC freezer in the following box (Google Sheet):

from Sam’s Notebook https://ift.tt/2CePNd2
via IFTTT