normalize and compare bigwig files

Question

[Bogdan]

Dear all,

I have received a few bigwig files that I would like to normalize and compare.

I am not very sure whether the bigwig files have been normalized already (for example by using deeptools).

Do you have any suggestions on the methods that I can use to normalize and contrast these bigwig files ?

Thanks,

Bogdan

Answer 1

[Matthias Zepper]

As you are probably aware, a BigWig file is nothing else than a numeric signal track, which can be converted back and forth between other formats such as BedGraph and Wiggle.

To assess if they have been normalized, you can e.g. try to map them with bigWigAverageOverBed (from UCSC tools) to a set of bed coordinates. If you happen to obtain the same values, then the files likely have been normalized with regard to those intervals before. But since there are various normalization strategies, such as effective genome size, you will never know for sure if they were not normalized or just normalized using a different strategy.