sum counts in regions in bed format

Question

[qwzhang0601]

I have processed the DNA methylation data and generate the file showing read count that call each CpG site as methylated or unmethylated. Now I want to sum such read counts in sliding windows. Is there some tools can do this easily? Briefly, for each window I will need to save the number of CpG sites covered, the sum of methyCount and unMethyCount.

#the file I generated is in the format as below
ChrID position methyCount unMethyCount
1       13823   0       1
1       13828   1       0
1       529822  2       0

#expected format for each window
Window      #CpG_covered      sum_methyCount sum_unMethyCount   
....

Thanks

[Ankit]

Hi,

If I correctly understood your query, one way I can think of:

Create you desired sliding window of genome (bedtools makeWindows). eg. 20 Kb may be. => File1.txt,

Your bed file of CpGs => File2.txt

Perform bedtools intersect File1.txt File2.txt. and concatenate the coordinates of CpGs by special character so that it become one string : chr1:1234:1234

Run aggregate function in R (see online examples)

[Ram]

What have you tried on your own?