item's end higher than chrom size, wigToBigWig

Question

[Samad]

Hello everyone,

When converting from wig to bigwig (*bw) using wigToBigWig program on hg19 genome

I got the following error:

bedGraph error line 30430242 of H3K36.wig: chromosome chr9_gl000201_random has size 36148 but item ends at 36160

How can the items end (in my wig) exceed the corresponding chrom size?

Thank you in advance for any help, suggestion...

Samad

Answer 1

[cmdcolin]

I think you can add the -clip option to the command line

 -clip - If set just issue warning messages rather than dying if wig
         file contains items off end of chromosome.

[Samad]

That worked thank you a lot!!

I didn't know that this option could skip the errors

So it shows me the errors of chrom size but the conversion continues and the bw file is created

Thanks again

Cheers

[matteo.zoia]

Hi, I have the same problem, where should I insert the -clip in order to avoid the problem? Just after the utility?

./wigToBigWig -clip file.wig chromsize.txt output.bw

Best