NSA2013_poster

__**Supporting Data for DNA Methylation Patterns in the Pacific Oyster (//Crassostrea gigas)//**__ 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.

Total number of aligned reads: Pairs=85 million Singles=32.4 million [|Output file]
 * Bisulfite Sequence Mapping Program (BSMAP):**

123 million covered cytosines Average coverage: 11.86 fold [|Output file]
 * Python methratio script**

1 million methylated CpGs Output file 2.9 million unmethylated CpGs Output file
 * Galaxy Workflow**
 * Note: methylated CpG= 5x coverage and at least 50% methylation

[] fuzznuc on oyster.v9_90 fasta file.
 * [Track] oyster.v9_90 all CGs **

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.

DNA Methylation Patterns in Crassostrea gigas. Claire Ellis, Steven Roberts. []
 * Electronic version of this poster available via figshare.**