Hyper-splitting

Posted by & filed under Cgigas DNA Methylation.

With a good two weeks hands-off of the the array data it took a bit of time to get back on target. Following up from last time (per my instruction) I began to delve into how the hypomethylated versus hypermethylated DMLs played out with respect to genomic features. Still not convinced I am convoluting the… Read more »

Where are they now?

Posted by & filed under Cgigas DNA Methylation.

tldr In an effort to find out where heat stress induced differentially methylated loci are in the oyster genome (to ultimately inform on function) I have been using bedtools to see where the DMLs lie on the genome. As this was done on an array platform I also felt I need to take into consideration… Read more »

Differentially methylated loci – repeats or TEs

Posted by & filed under Cgigas DNA Methylation.

In our original effort (bioRxiv doi:¬†http://dx.doi.org/10.1101/012831) 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 »