bigWig_an error in UCSC genome browser

[taehee]

Hi all,

I made a bigWig file from a published ChIP-Seq data using Homer software. And, I uploaded the "trackfileoutput.txt" to UCSC genome browser (on "Paste URLs or data" in Add Custom Tracks). But, I got an error message such as "Error https://dl.dropboxusercontent.com/u/...ucsc.bigWig.bw is not a big wig file").

The "trackfileoutput.txt" contains the header information that is uploaded as a custom track to UCSC at below;

track type=bigWig name="tag_forebrain Total Tags = 5.96e+06, normalized to 1.00e+07" description="tag_forebrain Total Tags = 5.96e+06, normalized to 1.00e+07" bigDataUrl=https://dl.dropboxusercontent.com/u/167314749/tag_forebrain.ucsc.bigWig.bw color=15,94,94 visibility=full yLineOnOff=on autoScale=on yLineMark="0.0" alwaysZero=on graphType=bar maxHeightPixels=128:75:11 windowingFunction=maximum smoothingWindow=off

And as an example, the format of the "tag_forebrain.ucsc.bigWig.bw" is at blow;

chr1 3000020 3000136 1.45
chr1 3000197 3000313 2.89
chr1 3000940 3001056 1.45
chr1 3001085 3001201 2.89
chr1 3001741 3001857 1.45
chr1 3005707 3005823 1.45
chr1 3008543 3008659 1.45
chr1 3010571 3010687 1.45
chr1 3013107 3013190 1.45
chr1 3013190 3013223 2.89
chr1 3013223 3013233 1.45

Does anyone know about this type of issue? Please share your information to resolve my problem. Thank you.

taehee

[blancha]

That is indeed not a bigWig file.
It's a bedGraph file.

A bedGraph file is a text file.
A bigWig file is the binary version of a bedGraph file.

UCSC has a command line utility to convert bedGraph files to bigWig files, called bedGraphToBigWig.

You can also view the bedGraph file in the UCSC Genome Browser, by changing the track type to bedGraph.
The bigWig files, however, are smaller and indexed, therefore much faster to load and view.

[taehee]

Thanks a lot blancha! I've uploaded my file as the bedGraph. But, I have one more question for you.

To convert bedGraph to bigWig, I've downloaded the bedGraphToBigWig from UCSC. And I run the program;

Taehyuks-MacBook-Proesktop Taehyuk$ bedGraphToBigWig tag_forebrain.ucsc.bedgraph mm10.chrom.sizes tag_forebrain.ucsc.bigwig

But, I get an error like at below;

tag_forebrain.ucsc.bedgraph is not case-sensitive sorted at line 2003164. Please use "sort -k1,1 -k2,2n" with LC_COLLATE=C, or bedSort and try again.

Could you please give me a hint how I can resolve this issue?

Many thanks!

taehee

[blancha]

The error message could be correct.
Just check lines 2003163 to 2003165, to determine the problem.

sed -n '2003163, 2003165'p file.bedgraph

If you see that the only problem is that the chromosomes are not in case-sensitive lexicographical order, just sort them.

LC_COLLATE=C sort -k1,1 -k2,2n file.bedgraph > file_sorted.bedgraph

[taehee]

Thank you very much for your helps! Now, everything is fine.