Hi all,
Wonder if anyone has retrieved CREs from the ENCODE III dataset on the SCREEN server: https://screen.encodeproject.org/
I'm trying to get a set of CREs with information on their H3K4me3, H3K27ac and DNase etc scores by providing a .bed file to the server. There's a few issues:
1) SCREEN doesn't seem to return more than ~900 CREs via the .bed route, this means you have to split big bed files into blocks - v. time consuming to figure out this issue! Hope no one else goes through this trauma down the line...
2) SCREEN doesn't provide Z scores for any of the histone mark or CTCF ChIPseqs in the bed file that it gives to you.
3) SCREEN doesn't let you filter the results you get back using any of the DNase or ChIPseq Z scores - this means you can't see which CREs have which Z scores without looking at them one by one on SCREEN server!
I can't proceed with what I want to do without info on the histone marks... quite frustrating!
Will be trying to get in touch with the authors but thought I'd post here in the meantime if anyone has any experience of using (or even setting up?) the SCREEN server and has suggestions for anything that I'm missing here?
Gracias
