Compile list of oyster DNA Methylation data sets

[sr320]

Will compile list of raw data from oysters that might be helpful in analysis...

To get started here is a page where I have compiled what we should have and links to genome viewer files.

http://onsnetwork.org/halfshell/2015/06/22/first-steps-at-an-aggregated-view-of-all-dna-methylation-data/

[sr320]

Will use this as a test of our data management system - https://github.com/sr320/LabDocs/blob/master/DMPseq.md

Library Database https://docs.google.com/spreadsheets/d/1r4twxfBHpWfQoznbn2dAQhgMvmlZvQqW9I2_uVZX_aU/edit

A quick count puts it at 13 libraries with C. gigas that were examined for methylation (and 6 C. virginica).

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Now using the Nightingales Database I come up with 43.

https://www.google.com/fusiontables/DataSource?docid=13IxnqIZ_2Xpz_HE-3YcnU_egASYz9ZlA0PYIDGLN

One issue is PE are separate.

BRB

[sr320]

One option if you wanted data where genome status is similar to geoduck- could use Olympia oyster data. Described - https://github.com/RobertsLab/project-olympia.oyster-genomic/wiki/MBD-BSseq-December-2015

Data - http://owl.fish.washington.edu/nightingales/O_lurida/20160203_mbdseq/

[sr320]

Corresponding Draft Genome Scaffolds: http://owl.fish.washington.edu/O_lurida_genome_assemblies_BGI/20160512/Ostrea_lurida.scafSeq