Alternative splicing and germline methylation

Posted by & filed under Cgigas DNA Methylation.

One of the premises related to germline methylation in oysters is that genes with limited methylation will have more alternatively spliced products. One of our most robust identification of alternatively spliced genes is from the heat shock experiment, however methylation was assessed with array to ID DMRs. In order to gauge the relationship of germline… 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 »

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 »

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 »

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 »

Splicing around

Posted by & filed under Cgigas DNA Methylation.

Here I am going to see to what degree I can identify differential splicing events that occur upon acute heat stress with the ultimate goal of determing if there is a relationship with differentiall splicing and DMLs. As the Tophat suite was used for RNA-seq, I will start exploring the cuffdiff output. Note all output… Read more »

Re-defining Cgigas Canonical features

Posted by & filed under qdod.

Below is an updated version of canonical genome tracks as part of the qdod project – @ github. Updates include details on version 25 gff files and adding the TE track derived via WU-Blast. Canonical Feature Tracks (Ensembl) Ensemble provides a feature tracks that are updated on a regular basis. They can be directly accessed… Read more »

Heating up the beds

Posted by & filed under Cgigas DNA Methylation.

tldr – RNA-seq feature tracks In an effort to better visualize the RNA-seq data from the heat shock experiment all accepted_hits.bam files from tophat2 analysis of the 6 libraries (3 pre, 3 post) were converted to bedgraphs. As per IGV recommendations, files were further converted to .tdf files. I tried to do this at the… Read more »