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 »

Developing CpG O/E Workflow

Posted by & filed under Workflows.

In an effort to streamline CpG O/E determination across various transcriptomes, here is my latest attempt. tldr; Ahyacinthus = This is dependent on have GO slim annotations for all genes – for this particular case the annotation pipeline can be seen here.