How do methylQA determine uniquely mapped fragments?
methylQA use a mapping quality 10 as cutoff, an alignment with mapping quality greater than or equal to 10 would be treated as unique alignment. This could be controlled by -Q option.
Where could I download the chromosome size file, CpG bed file and MRE fragments file?
We have prepared the files for Human hg19 for downloading at Install page, for other assembly, please contact us, we would be happy to provide them.