I have around 42 methylome files in both bedgraph.sorted and .wig form, but for the analyses I wish to run, I need the files in .cov form. Does anyone know how I can convert my files?
Where is the documentation for .cov format? I have never used it.
Sorry, .cov refers to coverage file types. I need this specific file type in order to import my files in BiSeq. They can be created with Bismark: https://rdrr.io/bioc/BiSeq/man/readBismark.html
I assume the bedGraph has the format:
chromosome start_position end_position methylation_percentage
While the .cov file you need has format
chromosome start end methylation_percentage count_methylated count_unmethylated
To get the methylated and unmethylated counts information:
a. If you have alignment files, you can use the bismark bismark2bedGraph utility to get .cov files.
b. If you have total aligned read counts per position and methylation percentage information, you can easily calculate count methylated and count unmethylated for .cov file as below:
count_methylated = methylation_percentage/100 * total_counts
count_unmethylated = total_counts - count_methylated
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