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):

• 20180709_emu_oly_methylation_mapping.ipynb

Genome used:

• Olurida_v080.fa ( run was initiated prior to creation of v081; see Genomic Resources wiki for more info )

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:

• owl/Athaliana/20180709_oly_methylseq

Bismark Summary Report:

• 20180709_oly_methylseq/bismark_summary_report.html

Individual Sample Reports:

• 1_ATCACG_L001_R1_001_trimmed_bismark_bt2_SE_report.html

• 2_CGATGT_L001_R1_001_trimmed_bismark_bt2_SE_report.html

• 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2_SE_report.html

• 4_TGACCA_L001_R1_001_trimmed_bismark_bt2_SE_report.html

• 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2_SE_report.html

• 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2_SE_report.html

• 7_CAGATC_L001_R1_001_trimmed_bismark_bt2_SE_report.html

• 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2_SE_report.html

• zr1394_10_s456_trimmed_bismark_bt2_SE_report.html

• zr1394_11_s456_trimmed_bismark_bt2_SE_report.html

• zr1394_12_s456_trimmed_bismark_bt2_SE_report.html

• zr1394_13_s456_trimmed_bismark_bt2_SE_report.html

• zr1394_14_s456_trimmed_bismark_bt2_SE_report.html

• zr1394_15_s456_trimmed_bismark_bt2_SE_report.html

• zr1394_16_s456_trimmed_bismark_bt2_SE_report.html

• zr1394_17_s456_trimmed_bismark_bt2_SE_report.html

• zr1394_18_s456_trimmed_bismark_bt2_SE_report.html

• zr1394_1_s456_trimmed_bismark_bt2_SE_report.html

• zr1394_2_s456_trimmed_bismark_bt2_SE_report.html

• zr1394_3_s456_trimmed_bismark_bt2_SE_report.html

• zr1394_4_s456_trimmed_bismark_bt2_SE_report.html

• zr1394_5_s456_trimmed_bismark_bt2_SE_report.html

• zr1394_6_s456_trimmed_bismark_bt2_SE_report.html

• zr1394_7_s456_trimmed_bismark_bt2_SE_report.html

• zr1394_8_s456_trimmed_bismark_bt2_SE_report.html

• zr1394_9_s456_trimmed_bismark_bt2_SE_report.html