How To Generate A Wiggle Output On Macs 2.0

Question

[Hamilton]

On MACS2.0, it seems there is no option for output wiggle file unlike previous versions with -S, --wig -w. is there any way to generate a wiggle output from ./macs2?

THanks.

Answer 1

[Ian]

If you use the -bdg flag you get a bedgraph file, which is almost exactly the same as a wig file. The difference is that if there are a set of adjacent positions with the same value they will be represented as a range, e.g. chr1 1000 1200 2. Wig would have 200 coordinates if value 2. See here for a better explanation.

You can use your bed graph file with wigToBigWig.