Do you have any particular questions about the analysis, or do you just need some help getting started?
For the latter, here's an example that might help you out: https://usegalaxy.org/u/james/p/exercise-chip-seq
I have a question about running MACS tool for my chip-seq data to call the peaks in Galaxy.
My data is pair-end sequenced. I have already upload the BAM mapping file I want to run MACS tool under the “Paired End Sequencing” but it asks for the ELANDMULTI format and for tow ChIP-seq Tag files.
How can I get the ELANDMULTI format dataset ? Do I only map each file Fastq R1 and R2 before starting MACS tool ?