Reviewer response for version 1
The authors have made a pipeline integrating differential RNA-Seq expression analysis with ChIP-Seq analysis and implemented it through the GenomeSpace platform. 
Though as mentioned by the authors in the paper: this is a commonly performed bioinformatic task, their aim is to make this integrated analysis easily accessible to non-bioinformatic users. 
For this purpose their workflow on the web-based workbench involves integrating multiple tools like Cuffdiff module in GenePattern (for Differential RNA-Seq analysis) with MACS2 in Galaxy (for ChIP-Seq analysis).
Though the workflow presented by the authors seems easy to use by any biologist, it also appears to be severely limited not just in its scope of application but also in its choice of tools which are hardcoded. 
For example the authors use "CuffDiff" for Differential RNA-Seq expression analysis. 
The authors do not state why they chose this particular method or even why they chose its GenePattern module and not the Galaxy implementation. 
Though admittedly this is a popular tool and has the advantage of transcript level analysis, it also suffers from known limitation of underestimating the number of differential genes. 
Other count based method like DESeq2 tool (also implemented in Galaxy) might be better suited for most gene-level differential RNA-Seq analysis. 
Also, the authors do not clearly explain why their workflow is better or easier for a biologist to implement than using the same tools through Galaxy directly (which has been made for a non-coding biologist). 
I would argue that working directly on Galaxy even if slightly more complicated would be more rewarding to users as it offers not just greater flexibility of tools but also the option to select different parameters than default.
Hence in conclusion, to make this manuscript better the authors should 1) provide a clearer explanation for their choice of tools and why is it easier/better to use their pipeline than the same tools on Galaxy directly, 2) If possible the authors should try to expand their workflow to provide a greater flexibility to the user to choose their tools for RNA-Seq and ChIP-Seq analysis.
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