Major Compulsory Revisions There are several key issues should be addressed:

1. At the very least a readme.txt should be provided to guide the data set as it’s currently very difficult to sort out all those files uploaded, and the SAM files after alignment that have been uploaded (as the authors claimed) are missing, or we can’t find them.

2. FASTQ files after LifeScope TM preprocessing were provided, but what about the data quality for the raw data? I highly recommend the authors to upload the raw fastq file.

3. What’s the reason for a very low alignment rate, i.e., 26.5%?

4. It was claimed replicate analysis for JWL using 1ug and 5ug DNA was performed, but what was the result of this?

5. When the authors claim “a significant number of peaks were common”, how do you define “common”?

6. Analyses on the correlation between Infinium 450K and SOLID MBD-Seq data is recommended.

Signed by Desheng Gong & Gao Fei

Level of interest An article of limited interest Quality of written English Acceptable Statistical review No, the manuscript does not need to be seen by a statistician. Declaration of competing interests I declare that I have no competing interests.

I think there is no serious issues should be addressed. Level of interest An article of limited interest Quality of written English Acceptable Statistical review No, the manuscript does not need to be seen by a statistician. Declaration of competing interests I declare that I have no competing interests