Annoying wigToBigWig err

[samad]

Hello,
I am facing the same problem when converting my wig file to bw and getting :
There's more than one value for chr1 base 876726 (in coordinates that start with 1).

[michaeltmccarthy]

There's more than one value for chr1 base 4710 (in coordinates that start with 1)??

Can anyone explain what this actually means? What is the problem with the file?

I've had this error trying to use wigToBigWig to convert a genome wide fixedStep wig file to bigWig format. When I load the chr1 wig file to the UCSC browser separately, the track displays just fine, and looking through the chr1 data, I can't see any problems around base 4710. The track only starts at chr1:10001... I've tried changing around my density script, but I've no idea what the problem is, and therefore no idea how to fix it.

And I can't find any wigToBigWig documentation that explains the meaning of the error!!

Any advice would be very very much appreciated!

Thanks in advance...

[JohnK]

How did you generate the wig file?

I got rid of the error I was receiving, but only after I separated each feature by the span length. I'm not sure why, but I've been playing the parameters for both variableStep and fixedStep, but I just can't get the data to stack the way I want to. Here's my current setup:

variableStep chrom=chr1 span=35
3001306 900
3002506 900
3002760 900
3012331 900
3012756 900
3014312 900
3015572 900


Getting this to work the way I want to is becoming a very tedious process.

I'm using that in combination with this when I upload the custom track:

track type=bigWig name="test" description="test" visibility=full autoScale=off maxHeightPixels=10:25:70 viewLimits=0:2 color=255,0,0 smoothingWindow=off graphType=bar

[dawe]

There's more than one value for chr1 base 4757310 (in coordinates that start with 1).


Checked the file and there are no duplicates. Has anyone gotten this error when converting from wig to bigWig before? Thanks.

John

I've faced the same issue with bedgraph files from FindPeaks 4. There are no easy solutions for this, you will probably need to write a check script that takes one of the values for that base position.
You may also try mergeBed from BEDTools to collapse overlapping regions into one, assuming your input is in bedgraph format and not wiggle.
d

[Thomas Doktor]

How did you generate the wig file?

[JohnK]

*I'm using the wigToBigWig' conversion script, btw.

[JohnK]

There's more than one value for chr1 base 4757310 (in coordinates that start with 1).


Checked the file and there are no duplicates. Has anyone gotten this error when converting from wig to bigWig before? Thanks.

John