Problems opening a WIG file in IGB

Question

[Iñaki]

Dear all,

I'm trying to open a wiggle file from a ribosome profiling study with IGB (It's the first time I'm using IGB).

For example, the GEO accession is: GSE53767.

I decompressed the ".wig.gz" file, but after trying to open it in IGB, it says:

Unable to load data set for this file.

After some searches, I found that a wiggle file should start with a declaration line like this:

variableStep chrom=chr1

This file didn't have it so I add this line, and then IGB was able to open it. But I wasn't able to load the data in IGB, it's like there was no data...

How can I properly open this file?

Thank you very much for your support.

Answer 1

[Asaf]

I guess that the name of the chromosome you entered is not the one IGB has. look at the right hand side of the screen and you'll see the names of the available chromosomes, see if yours is similar to the the one you're viewing. I had the same problem.

[Iñaki]

Yes, firstly I removed "chrom=chr1" and I was able to see the data (but without any sequences).

Then I put "chrom=NC_000913" and it works.

Answer 2

[Nowlan Freese]

Hello from the IGB team!

Iñaki and Asaf are exactly correct. Wiggle files require a declaration line that specifies variable versus fixed step, as well as the chromosome.

So for this example the declaration line would be:

variableStep chrom=NC_000913

[daniel.alameda]

I have the same issue with another files from GEO: GSM1163096 for example. The case is that I have no problem in opening this files with IGV program (without editing them). I wonder if there is a way to use this files without editing them. Thanks.

[Nowlan Freese]

Hi Daniel,

Thank you for pointing this out, as it is another interesting example of a file not following the standard format.

In the WIG file you mentioned (from GEO: GSM1163096), the issue is that partway through the file (line 2827115) it switches from WIG to BED format. IGB recognizes that there is an issue with the file and does not load it. IGV also recognizes the issue, but appears to ignore the data that doesn't match the WIG format.

I'm not sure why there is a BED file embedded in the WIG file, but if you remove the BED portion than the file will load correctly.