Bismark: bedgraph to bigwig for DNA methylation

Question

[pixie@bioinfo]

Hello, I have a small question. I want to convert the bismark coverage files to bigWig format. I have the sample_CHG.gz.bismark.cov files. Other than the first 3 columns which refer to the chromosome and coordinates, which of the last 3 columns I should keep as the score for the bedgraph ? Thanks.

SL4.0ch07       136     136     50      1       1
SL4.0ch07       153     153     100     2       0
SL4.0ch07       378     378     50      1       1
SL4.0ch07       380     380     100     2       0

Answer 1

[aconga]

The score is the 4th column. The 5th column reports methylated reads in that cytosine and the 6th column reports unmethylated reads in that citosine.

So you should only keep the first 4 columns when transforming that file into a bedGraph file.

Answer 2

[ATpoint]

bedGraph has four tab-separated columns, that is chr-start-end-value where value is any numeric value that you want. So you could simply use either the read counts of the Cs or a percentage or fraction of the methylated CpGs as value. From the normal bedGraph to bigwig tools apply, e.g. bedgraphtobigwig from kentUtils.