Question: wigCorrelate Error "Please remove overlaps and try again"
1
gravatar for ct13
4.7 years ago by
ct1310
United Kingdom
ct1310 wrote:

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

wigcorrelate • 1.8k views
ADD COMMENTlink modified 21 months ago by Samad90 • written 4.7 years ago by ct1310

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

ADD REPLYlink written 4.7 years ago by TriS3.9k
0
gravatar for wangyuting1482
3.8 years ago by
wangyuting14820 wrote:

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

ADD COMMENTlink written 3.8 years ago by wangyuting14820
0
gravatar for Samad
21 months ago by
Samad90
France
Samad90 wrote:

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

ADD COMMENTlink written 21 months ago by Samad90

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:

- General questions: genome@soe.ucsc.edu
- Questions involving private data: genome-www@soe.ucsc.edu
- Questions involving mirror sites: genome-mirror@ose.ucsc.edu

ChrisL from the UCSC Genome Browser

ADD REPLYlink written 21 months ago by genecats.ucsc560
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