Hello, I have some ChIPseq data but I do not know how to write/use code so I am trying to build a workflow on UseGalaxy.org to analyze Treatment-vs-Control in 3 biological replicates sequenced on Illumina. Based on some of the online forums, I need to "intersect" (and not "merge") the data between 3 biological replicates.
1) On pipeline design: - Do I need to fist run the intersct of 3 dataset (e.g. 3 treatments, 3 control), then run the output of 3 treatment against the output of 3 controls on MACS. - or, do I need to first run MACS on Treatment vs Control for each biological replicate, then run intersect on the output files.
2) On the use of the Multiple Intersect function (under BEDTools) in building a Workflow: How to I compare 2 or 3 files if the total allowed input is 1 BED file and 1 genome file? Am I misunderstanding what the purpose of the tool is?
Any expert opinion would be greatly appreciated! Dan