bedgraph.sorted or wig to .cov files?
1
0
Entering edit mode
14 months ago
arshkhaira ▴ 10

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?

coverage bedgraph.sorted bedgraph wig • 430 views
ADD COMMENT
0
Entering edit mode
ADD REPLY
0
Entering edit mode

Where is the documentation for .cov format? I have never used it.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
2
Entering edit mode
14 months ago
Shalu Jhanwar ▴ 500

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
ADD COMMENT

Login before adding your answer.

Traffic: 1682 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6