wigToBigWig error

[Fu, Xiaoyong]

Hello,

I am using the UCSC wigToBigWig but encountered the following error:

line 5421388 of /Volumes/LaCie/NGS100_analysis_7-9-2018/XF11_filtered.wig: chromosome chr10 has 135534747 bases, but item ends at 135534750

My command line is:

./wigToBigwig *.wig "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.chrom.sizes" *.bw

The head of my wig file is:

 

fixedStep chrom=chr10 start=1 step=25 span=100

0.000

0.000

0.000

0.000

0.000

0.000

0.000

0.000

0.000

Thanks for your help!

Best,

Xiaoyong Fu

Baylor College of Medicine

[Brian Lee]

Quote Edit Delete

Dear Xiaoyong Fu,

Thank you for using the UCSC Genome Browser and your question about the error message you are seeing.

It can be helpful at times to run the command without any arguments to review the options. For example, here is the wigToBigWig command showing it's options including the "-clip" option that could be of interest:

$wigToBigWig 
wigToBigWig v 4 - Convert ascii format wig file (in fixedStep, variableStep
or bedGraph format) to binary big wig format.
usage:
   wigToBigWig in.wig chrom.sizes out.bw
Where in.wig is in one of the ascii wiggle formats, but not including track lines
and chrom.sizes is a two-column file/URL: <chromosome name> <size in bases>
and out.bw is the output indexed big wig file.
If the assembly <db> is hosted by UCSC, chrom.sizes can be a URL like
  http://hgdownload.soe.ucsc.edu/goldenPath/<db>/bigZips/<db>.chrom.sizes
or you may use the script fetchChromSizes to download the chrom.sizes file.
If not hosted by UCSC, a chrom.sizes file can be generated by running
twoBitInfo on the assembly .2bit file.
options:
   -blockSize=N - Number of items to bundle in r-tree.  Default 256
   -itemsPerSlot=N - Number of data points bundled at lowest level. Default 1024
   -clip - If set just issue warning messages rather than dying if wig
                  file contains items off end of chromosome.
   -unc - If set, do not use compression.
   -fixedSummaries - If set, use a predefined sequence of summary levels.
   -keepAllChromosomes - If set, store all chromosomes in b-tree.

An engineer looking at your example file noticed that you have invalid input. The sample wig ascii shares a step of 25 and span of 100. The wiggle format does not work that way. One could have a step of 100 and a span of 25, but not the other way around.

Here is more about the wiggle format: http://genome.ucsc.edu/goldenPath/help/wiggle.html

fixedStep chrom=chr3 start=400601 step=100
11
22
33
displays the values 11, 22, and 33 as single-base regions on chromosome 3 at positions 400601, 400701, and 400801, respectively. Adding span=5 to the declaration line:

fixedStep chrom=chr3 start=400601 step=100 span=5
11
22
33 
causes the values 11, 22, and 33 to be displayed as 5-base regions on chromosome 3 at positions 400601-400605, 400701-400705, and 400801-400805, respectively.

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further public questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee
UC Santa Cruz Genomics Institute

--

---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome-mirror+unsubscribe@soe.ucsc.edu.
To post to this group, send email to genome...@soe.ucsc.edu.
Visit this group at https://groups.google.com/a/soe.ucsc.edu/group/genome-mirror/.
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/7F417386-1AB6-4E69-ABDA-ED0C1837A1D0%40bcm.edu.
For more options, visit https://groups.google.com/a/soe.ucsc.edu/d/optout.