I try to use ENCODE annotation data in my own data analysis. I couldn’t find a introductory tutorial on ENCODE data access and usage. So I explored a little on myself.
I found that the old data of ENCODE production phase (2007-2012) can be viewed and accessed from UCSC: http://genome.ucsc.edu/ENCODE/downloads.html
And newer data can be accessed at their new portal: https://www.encodeproject.org/
however, there is no simple and intuitive way to view and access at this new ENCODE project portal as from UCSC portal. Their programmatic access intro is a bit heavy and not informative. I don’t even find where are processed and integrated data like those from UCSC. Can anybody help on this or point to the right direction? Thank you!
BTW, I noticed that AnnotationHub provide ENCODE data, do AnnotationHub data include UCSC data but not the newer ones?