Finishing out with the mechanical

Posted by & filed under Ostrea lurida.

Currently there is a pretty robust spreadsheet and over the past few days Jake has cranked through some reps to see how the oysters that were mechanically stressed hold up. Below is how these data are integrated. Currently the 8-10 samples (yellow) have been skipped, but we might have a look. First up is having… Read more »

Second look at Geoduck transcriptome

Posted by & filed under Panopea generosa.

Last week I popped out a quick assembly and annotation on our geoduck gonadal transcriptome. A second assembly was also done using Trinity. Updates August 3 – Confirmed // in file location had no impact on assembly. July 14 – TransDecoder protein annotations 10:40am – added TransDecoder results 10:29am – added Stats via Trinity Output… Read more »

A closer look at DMRs

Posted by & filed under Cgigas DNA Methylation.

A detailed look at DMRs that hold true across oysters exposed to heat shock. Updated July 6, 2015 – added three more DMRs (at bottom of post) Going down the list, scaffold418_576986 is a feature that overlaps gene EKC36328, Bromodomain-containing protein 8. Specifically the location is in the intron between exon 18 and 19 (total… Read more »

First steps at an aggregated view of all DNA methylation data (updated)

Posted by & filed under Cgigas DNA Methylation.

Seems like I have gotten close (see here) but do not have a canonical IGV session that has all of our DNA methylation data. The goal here is to generate such a product (and publish, so I do not lose it). All data is publicly available at http://owl.fish.washington.edu/halfshell/index.php?dir=2015-05-comgenbro see also data on Figshare Updates July… Read more »