Hello, I have been provided with methylation txt files for target_regions that look like this:

chr position meth unmeth total degree.of.meth
chr1 1058346 1 1 2 0.5
chr1 1058391 1 0 1 1
chr1 1058414 1 0 1 1
chr1 1058439 1 0 1 1
chr1 1058481 2 0 2 1

I merged them into one big file that has positions as rows and samples as columns. To use Bsmooth I need to provide also a coverage matrix.

The files provided are target_region methylation files, and i need to use those. Also, I have region_of_interest methylation files in another folder (that another person has analyzed). There is a coverage matrix inside the region of interest files folder. Can I use that matrix as coverage for my target_region files? or should there be a coverage matrix file for target_region and another for region_of_interest?

I am new to this so I don't know if the coverage matrix has been created when all the methylation files were created (with bismark or something like that) or if that matrix has been created specifically from/for the region_of_interest methylation files.

This is what the coverage matrix looks like:

seqnames    start   sample1 sample2 sample3 sample4 sample5 sample6 sample7 sample8 sample9 sample10    sample11    sample12    sample13    sample14    sample15    sample16
chr1    1058346 3   1   4   1   2   3   5   2   4   3   6   2   7   4   2   2
chr1    1058658 4   0   4   1   6   3   1   1   4   2   7   2   0   5   4   1
chr1    1058677 3   2   4   1   6   3   3   2   5   3   9   4   4   3   6   3
chr1    1058688 2   4   5   1   5   2   4   1   4   5   7   3   7   3   6   2

Thank you