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
didn't you ask this question yesterday? How to proceed from these methylation .txt files?
No, this is about the coverage matrix. I know what to do next but not what coverage matrix to use