Three workflows for first-level analysis of ChIP-seq data is now available in our local Galaxy server (go to Shared Data > Published Worflows).

These workflows perform QC analysis (fastqc, spp cross-correlation), read mapping with bowtie2, read filtering (for unmapped reads, duplicates and mutli-mapping reads), peak calling with MACS1.4, visualization files creation (lib size normalized, bg subtracted and log ratios) and replicate correlation

And best of all, all generated files have meaningfull names (yes it is possible to do this in Galaxy workflows) provided you started with nicely named fastq files, and are automatically copied in a smart directory architecture created on your file server in the directory of your choice (thanks to our improved NFS transfer Galaxy tool). 

Important : these worflows can be use as such for the fly but must be copied and their parameters adapted if you use another organism! 

More details about these workflows at the Galaxy Workflow page

Happy analysis !