Monthly Archives:: June 2015

Side track with tracks

Posted by & filed under Cgigas DNA Methylation.

Today working on our paper looking at heat stress and DNA methylation I dived deeper into the array data in the search for what should be called a DMR. As a refresher we have tracks from the core that have 1.8+ fold difference (sig) and complementary tracks where there are three adjacents (3plusAdjacent). I made… Read more »

Passing Flanks

Posted by & filed under Ostrea lurida.

A first look at population differences at qPCR primer sites for three population of Olympia oysters Plate 1 (samwhite_112381) included, BMP2, CARM, HSPb11, and PGEEP4. At the bottom is a full list of qPCR primers. BMP2 Limited coverage CARM Better coverage conflicts were ambigs (ie S,W,R) HSPb11 Missed qPCR primer (R did not seem to… 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 »

Quick Carmalign

Posted by & filed under Ostrea lurida.

The first batch of sequencing came into today to verify sequence of Olympia oyster qPCR primers. 1) imported .ab1 files into CLC, 2) trimmed “CARM” sequences 3) aligned to comp7220_c0_seq2

Wayback to just-MBD

Posted by & filed under Cgigas DNA Methylation.

Prior to bisulfite sequencing we did do a couple of MBD enrichment libraries to describe DNA methylation in oysters. Results even were snuck into this perspective. While I am sure there are genome tracks around, I am ending up #doingitagain. In short I took the raw Solid reads, align to Crassostrea_gigas.GCA_000297895.1.26.dna.genome in CLC, exported bam,… Read more »