Hey, just a quick question,
So I have some RRBS data that I downloaded from SRA ( matched normal tumor pairs ) which I want to analyze to gain some experience working with this type of data. I decided to use bismark for aligning followed by metilene for DMR identification. While aligning in bismark, I saw there was an option
--non_directional to specify if the reads came from a non-directional library. Here is the publication containing the data whose methods refer to this paper for the library prep. Now reading the Material and Methods section, I got no idea if it is a directional prep or not.
Is there a way to figure out what is the directionality of the data? (Although the bismark documentation says that most Illumina RRBS preps are directional and
--non_directional is set to OFF by default).
By running the same sample in both directional and non-directionalmode, can I figure out the directionality?
Thanks a lot for your help. Cheers.