Question: Coverage of methylation txt files
0
gravatar for Pin.Bioinf
21 months ago by
Pin.Bioinf260
Malaga
Pin.Bioinf260 wrote:

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

bismark coverage methylation • 688 views
ADD COMMENTlink written 21 months ago by Pin.Bioinf260

didn't you ask this question yesterday? How to proceed from these methylation .txt files?

ADD REPLYlink written 21 months ago by Martombo2.6k

No, this is about the coverage matrix. I know what to do next but not what coverage matrix to use

ADD REPLYlink written 21 months ago by Pin.Bioinf260
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