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How To Generate A Wiggle Output On Macs 2.0

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.

macs chip-seq

1 answer

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.

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