How to read a Wig file format of Histone modification

Question

[Zakaria Benmounah]

Hi,

How to read a Histone modification file in Wig format?

I've found general explanation about the Wig Format here, but I'm looking for one specific to Histone modification. What does the integer value mean?

This is an example of Histone modification in Wig file format:

track type=wiggle_0 name="UCSD.Aorta.H3K27me3.STL003" description="UCSD.Aorta.H3K27me3.STL003" visibility=full color=20,150,20 track_id=NA000008237.1 taxon_id=9606 genome_id=GCF_000001405.13
fixedStep chrom=chr1 start=10001 step=20 span=20
0
7
7
8
9
9
9
10
12

Cheers

Answer 1

[Ryan Dale]

It very much depends on the lab that created the data.

If it's from ChIP-seq data, a WIG file could have the number of reads (possibly with each read extended 3' to be the size of an average fragment in the library). It may or may not be scaled to library size or scaled to other tracks in the same experiment. If it's ChIP-chip, then the numbers could be log2 ratio of IP to input.

Since the numbers you're showing are integers, my guess is that these values are raw read counts that are neither scaled to library size nor normalized by control. But to find the actual answer, you need to look closely at the methods of how the track was created. If that information isn't available, you'll need to contact the authors.