wigCorrelate Error "Please remove overlaps and try again"

Question

[ct13]

Hi there,

I tried to use wigCorrelate to correlate the two ChiP-seq wig files I generated by MACS1.4, but I ran into an error:

The wig files contained is variable step and contain all chromosomes.

Overlap on chr1 between items starting at 19999990 and 20000000.
Please remove overlaps and try again

It is very strange as when it exceeded the chr1 length and either of my two wig files have lines in chr1 at this position.

The same error message recurr even if I tried wigToBigwig.

Please help!

J

[TriS]

not sure if this will solve it but it's prob worth a try (thank you Google):

https://code.google.com/p/biotoolbox/issues/detail?id=3

[wangyuting1482]

for this question "wigError", are you solving it?? if yes, how to deal with. Now i got the same trouble. Thank you!!

[Samad]

I have the same error when converting wig to bigwig :Overlap on chr1 between items starting at 0 and 0

wig head:

variableStep chrom=chr1
3003560 0
3003561 0
3003562 0
3003563 0

[genecats.ucsc]

Hi Samad,

wigToBigWig works fine for me with the following test wiggle file:

$ cat test.wig 
variableStep chrom=chr1
3003560 0
3003561 0
3003562 0
3003563 0
$ wigToBigWig test.wig hg38.chrom.sizes out.bw

What commands are you running to generate a bigWig?

Additionally, the whole point of variableStep wiggle format is to condense the file. The above example can be more succinctly written as:

variableStep chrom=chr1 span=4
3003560 0

If you have further questions about UCSC data or tools feel free to send your question to one of the below mailing lists:

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ChrisL from the UCSC Genome Browser

[wjyzidane]

Try mergeBed -c 4 -o mean -d -1 options.