bigwig to wig conversion

Question

[jmack159]

I am trying to convert a bigwig file to a wig file to run through sitepro. I tried using the ucsc tool bigWigToWig and I get a file that looks like this:

#bedGraph section chr1:0-3079820
chr1    0    3001030    0
chr1    3001030    3001060    2.41
chr1    3001060    3001230    4.83
chr1    3001230    3001270    2.41
chr1    3001270    3002330    0
chr1    3002330    3002380    4.83
chr1    3002380    3002540    9.65
chr1    3002540    3002590    4.83
chr1    3002590    3003210    0

However, sitepro is choking on this wig file. I normally use wig files generated by MACS, which have a much different formatting:

track type=wiggle_0 name="macs_output_treat_all" description="Extended tag pileup from MACS version 1.4.2 20120305 for every 10 bp"
variableStep chrom=chr1 span=10
3001071    1
3001081    2
3001091    2
3001101    2
3001111    2
3001121    2
3001131    2
3001141    2

Why is the ucsc bigWigToWig tool giving me a bedgraph file rather than a wig file?

Answer 1

[Dan D]

This guy experienced the same problem, and has an answer (and a script to go from bedGraph to wig) on his site:

http://sebastienvigneau.wordpress.com/2014/01/10/bigwig-to-bedgraph-to-wig/

[jmack159]

Thanks! That script worked beautifully!