How to convert .wib files to .wig or .bed?

Question

[Zeng Jingyu]

Hi everyone, I'm recently work on a project using genome traits. I need to convert .wib format files to .bed files. But I can't find any software doing this, even on UCSC. And I searched the website, found that years ago someone also asked this question but no one answered.

I hope someone can help us solve this problem.

[Carlo Yague]

From UCSC, use wigToBigWig then bigWigToBedGraph. There is also the wig2bed fonction in BEDOPS that does this in a single step. Other options are discussed in this post: Wiggle File 2 Bed File

[Zeng Jingyu]

I've tried your suggestions, but it seems that .wib file is the binary version of .wig file, and the softwares (BEDOPS and wigToBigWig) produced errors like "Unrecognized line" or "Error: Invalid WIG line 1".

I wonder if I did anything wrong?

[Carlo Yague]

My apologize, I read "wig" instead of "wib". I actually never heard of .wib. Hope someone else can answer you.

[Zeng Jingyu]

Fine, thank you anyway.

[Zeng Jingyu]

When converting .wig files to .bed files, your suggestion works. But when it comes to .wib files, the softwares start to produce errors.

Answer 1

[Alex Reynolds]

Perhaps use wibToWig to convert from binary to Wiggle, and then convert2bed --input=wig < foo.wig > foo.bed or wig2bed < foo.wig > foo.bed to convert from Wiggle to BED.

• https://github.com/dasmoth/wibToWig
• https://github.com/bedops/bedops

[Zeng Jingyu]

Thanks, but I've found the same file which is in .bw instead of .wig.

By the way, I don't know how to use this wibToWig. I don't understand what I should input.

But fine, everything is ok now.

[Maximilian Haeussler]

Can you say how everything is OK? Is this question not relevant anymore?

[Zeng Jingyu]

No, it's not because everything is done. As I mentioned, I found the same file in the format .bw instead of .wig. So I just skipped that question. And as I said, wibToWig still doesn't work.