Genomic features and workflow used for characterization of DNA methylation in the Pacific oyster genome [version oyster.v9_90 (fasta)]
This version of the genome represents the longest genomic scaffolds (1670; 14%) that covers over 90% of the genome.
Derived from the genome build available at:
Zhang, G; Fang, X; Guo, X; Li, L; Luo, R; Xu, F; Yang, P; Zhang, L; Wang, X; Qi, H; Zhu, Y; Yang, L; Huang, Z (2012) Genomic data from the Pacific oyster (Crassostrea gigas). GigaScience. http://dx.doi.org/10.5524/100030
This page also includes links to software, an electronic version of the poster presented at the NSA meeting, and other additional resources.
Bisulfite Sequence Mapping Program (BSMAP):
Total number of aligned reads:
Pairs=85 million
Singles=32.4 million
Output file
Python methratio script
123 million covered cytosines
Average coverage: 11.86 fold
Output file
Galaxy Workflow
1 million methylated CpGs
*Note: methylated CpG= 5x coverage and at least 50% methylation
Output file
2.9 million unmethylated CpGs
Output file
[Track] oyster.v9_90 all CGs
http://eagle.fish.washington.edu/Mollusk/174gm_analysis/Bedtools_Intersect/oyster.v9_90_allCGs
fuzznuc on oyster.v9_90 fasta file.
For additional tracks and analyses please visit:
http://genefish.wikispaces.com/Methylation+Patterns+in+the+Pacific+Oyster+Genome
Bedtools and SQLShare used to examine relationship in genomic features. David and Revigo was used for gene ontology and enrichment analyses.
Electronic version of this poster available via figshare.
DNA Methylation Patterns in Crassostrea gigas. Claire Ellis, Steven Roberts.
http://dx.doi.org/10.6084/m9.figshare.478021
