Since you’ve been gone

Posted by & filed under Cgigas DNA Methylation, Ostrea lurida.

Soon after Ensenada I went to Chili, SICB, and PAG (in that order). The new year is often of time to let go of lingering projects, and likely I will be doing that soon. But to bring a few pending efforts to the forefront, so that I can analyze etc here is a bit of… Read more »

There is something about TEs

Posted by & filed under Cgigas DNA Methylation.

For purposes of proposaling and reports, I have gone back to look at a small project done in collaboration with scientist at IFREMER looking at pesticide exposure on oyster larvae methylation. The control library had limited yield so the number of loci with data from the treated and the control library was restricted. However using… 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 see also data on Figshare Updates July… Read more »

Shortish list

Posted by & filed under Ostrea lurida.

In selecting qPCR targets from the Oly transcriptome (version 3) I came up with the following list. In general this was done by first focusing on stress response GO slim terms, followed by simple word searches. The table is available for download here The next step would be some joining & file converting to pull… Read more »

Differentially methylated loci – repeats or TEs

Posted by & filed under Cgigas DNA Methylation.

In our original effort (bioRxiv doi:¬† we characterized DMLs in relationship to genomic regions, including putative transposable elements. In this case TEs were defined as tandem repeats and targets that had sequence similarity to protein sequences in other species. Transposable elements were identified using RepeatMasker, a program that screens and annotates interspersed repeats (Smit et… Read more »

RNA-Seq: Tophat via iPlant

Posted by & filed under Workflows.

Goal: Use RNA-seq to compare expression between oysters (n=3) pre and post heat shock. Based on IPlant Collaborative Tutorial Task 1: Align read data to Crassostrea gigas genome. Tophat is a specialized alignment software for RNA-seq reads that is aware of splice junctions when aligning to a reference assembly. 1) Click Apps from DE… Read more »