Thanks alot, this was very helpfull to me aswell. To remove heades and combine the wig files in a bigwig file i used:

zcat *.wig.gz | grep -v ^track | wigToBigWig -clip stdin genome.table output.bigwig

Mvh Anders

If there is only one chromosome per file, you can just concatenate those wig:

cat chr*.wig > genome.wig

If you have multiple wig files (and MACS wig are gzipped) you should concatenate:

zcat *.wig.gz | wigToBigWig -clip stdin chromsizes.tab output.bigwig

If you have only one file (and macs14 allows this) you can directly go with

wigToBigWig -clip stdin chromsizes.tab output.bigwig

As recent wigToBigWig support gziped input.

In case you didn't already know MACS 1.4 beta has a function to create a single WIG file, use '--wig --single-wig'.

The important point is that you MUST remove the track header from the top of each WIG file before you merge them and convert them to bigWig. I like to keep a copy of the header.

Keep header:

head -n 1 *chr1.wig > header

Remove first line (track header):

sed -i '1d' *wig

Hope this helps!