I am interested in data deposited in GEO under GSE113047. I was hoping for a table of gene symbols and counts. Instead, there is a tar of .bed and .bedGraph files.
I have all sorts of questions.
Why would someone deposit bed and bedGraph files instead of a counts table? Is it more useful, or is it just easier?
Can I get a counts table out of these files?
Why are there two files? What does one do that the other doesn't?
bed files apparently contains a 'score' field. What is the meaning of that score?
bedGraph files apparently contain a 'dataValue' field. What is the meaning of that value?
What are "peaks"?
Do I need an external annotated genome to get counts of symbols? How would I know which reference genome to use?
Where can I find documentation that would explain these things?
Thanks so much, I'm finding this pretty confusing.