Question: Bigwig to bed conversion on Windows OS without command line
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gravatar for ahramkim1128
2.8 years ago by
ahramkim112810
United States
ahramkim112810 wrote:

Hi,

I am a fly geneticist and have no experience about programming language.

I saw several papers using ChIP-seq analysis and wanted to check whether some transcription factors bind to locus of my interest gene.

I downloaded seq data and tried to analyze it using EaSeq on Windows OS.

Unfortunately, EaSeq doesn't support bigwig format, which should be converted to other formats, such as wig or bed.

Is there any bigwigtowig or bigwigtobed conversion program without command line?

Command line would be a very big hurdle for basic biologist T^T.

Of course, I have plan to learn programming language, but it's hard for me to wait until I finish learning.

It will be very helpful for my future work if you suggest nice and simple conversion tool.

Thank you for your help in advance.

ADD COMMENTlink written 2.8 years ago by ahramkim112810
1

The easiest route would be to upload the files to Galaxy and have it do the conversion.

ADD REPLYlink written 2.8 years ago by Devon Ryan91k

There is a wig/bedgraph to bigwig, but bigwig to wig/bed. Could you inform the link (bigwig to wig)?

ADD REPLYlink written 2.8 years ago by ahramkim112810

Indeed, I guess the don't provide a converter. Just borrow someone's Mac then.

ADD REPLYlink written 2.8 years ago by Devon Ryan91k

What kind of analysis do you need to do in EaSeq? A bigwig should be able to be loaded directly to FlyBase or UCSC for visualization.

If you have your heart set on EaSeq, then you may be able to load the bigwig into UCSC and then use the Table Browser tool to download it as a bed file.

ADD REPLYlink written 2.8 years ago by ejm32440
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