Sicer questions
I am using Sicer to examine data from DNMT1 binding by ChIP-seq. I run IP and input and want to know
1) what is the ChIP island Read Count and Control island read count and how are they calculated.
2) Are these data normalized or do I need to do this separately if I have multiple samples? If the answer is yes- what do you recommend?
3) What are the redundancy raw reads (filtered by islands) and
4) Does anyone know of a ChIP-seq paper that has recently used this approach?
1) what is the ChIP island Read Count and Control island read count and how are they calculated.
2) Are these data normalized or do I need to do this separately if I have multiple samples? If the answer is yes- what do you recommend?
3) What are the redundancy raw reads (filtered by islands) and
4) Does anyone know of a ChIP-seq paper that has recently used this approach?