Fei Gao (Reviewer 1)

To demonstrate the usage of Methpat program, the authors provided data from sequencing of multiplex PCR products that targeted 48 regions of interest across 86 human samples. As indicated, the regions selected included known gene promoters associated with cancer, repetitive elements, known imprinted regions and mitochondrial genomic sequences. Furthermore, a range of samples including human cell lines, primary tumours and primary tissue samples were applied. These data are potentially interested for researchers who work on DNA methylation studies, especially who would like to check general methylation information of these regions. Methpat also seems to be a useful tool to extract and visualize massively parallel DNA methylation data, these data will be useful for the researchers who would like to use Methpat for data mining. I think this data can be considered for publication as data note in Gigascience before adding some supplemental information:
1, As indicated in the manuscript, fastq file should be uploaded into GEO, however, I can't find it. Not sure whether because I only have restricted access? Otherwise please upload them.
2, It was claimed that "the abundance of allelic patterns can be measured", are these data included in the output file about abundance of allelic patterns?
3, When the authors said "Methpat requires a BED-format like file that …", does it mean that Methpat uses a BED format to extract or locate some regions in alignment file? And is this BED-format file included in the uploaded file?
4, In the table listing all primer sequences, I suggest to indicate which genomic regions are targeted by each primer pair.

Level of interest: An article whose findings are important to those with closely related research interests
Quality of written English: Acceptable
Declaration of competing interests: I declare that I have no competing interests