Genes (RNA-Seq) on Oly Genome

Posted by & filed under Ostrea lurida.

We currently have a version (0.0.2) of the Ostrea lurida genome on CoGe. This is 38 scaffolds greater than 80k bp. Below is an effort to map gonad RNA-seq data to said genome. Two male gonad and two female libraries were mapped to the genome using TopHat in Cyverse Discovery Environment. Through the steps… I… 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 »