DNA Methylation Analysis - Bismark Pipeline on All Olympia oyster BSseq Datasets

2018
Miscellaneous
Author

Sam White

Published

August 16, 2018

Bismark analysis of all of our current Olympia oyster (Ostrea lurida) DNA methylation high-throughput sequencing data.

Analysis was run on Emu (Ubuntu 16.04LTS, Apple Xserve). The primary analysis took ~14 days to complete.

All operations are documented in a Jupyter notebook (GitHub):

Genome used:

Input files ( see Olympia oyster Genomic GitHub wiki for more info ):

WG BSseq of Fidalgo Bay offspring grown in Fidalgo Bay & Oyster Bay

  • 1_ATCACG_L001_R1_001.fastq.gz

  • 2_CGATGT_L001_R1_001.fastq.gz

  • 3_TTAGGC_L001_R1_001.fastq.gz

  • 4_TGACCA_L001_R1_001.fastq.gz

  • 5_ACAGTG_L001_R1_001.fastq.gz

  • 6_GCCAAT_L001_R1_001.fastq.gz

  • 7_CAGATC_L001_R1_001.fastq.gz

  • 8_ACTTGA_L001_R1_001.fastq.gz

MBDseq of two populations (Hood Canal & Oyster Bay) grown in Clam Bay

  • zr1394_10_s456.fastq.gz

  • zr1394_11_s456.fastq.gz

  • zr1394_12_s456.fastq.gz

  • zr1394_13_s456.fastq.gz

  • zr1394_14_s456.fastq.gz

  • zr1394_15_s456.fastq.gz

  • zr1394_16_s456.fastq.gz

  • zr1394_17_s456.fastq.gz

  • zr1394_18_s456.fastq.gz

  • zr1394_1_s456.fastq.gz

  • zr1394_2_s456.fastq.gz

  • zr1394_3_s456.fastq.gz

  • zr1394_4_s456.fastq.gz

  • zr1394_5_s456.fastq.gz

  • zr1394_6_s456.fastq.gz

  • zr1394_7_s456.fastq.gz

  • zr1394_8_s456.fastq.gz

  • zr1394_9_s456.fastq.gz

RESULTS:

With Bismark complete, these two sets of analyses can now be looked into further (and separately, as they are separate experiments) using things like MethylKit (R package) and the Integrative Genomics Viewer (IGV).

Output folder:

Bismark Summary Report:

Individual Sample Reports: