Bam to UCSC readable bed file

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hdaoud

Junior Member

Join Date: Aug 2013

Posts: 1
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#1

Bam to UCSC readable bed file

08-21-2013, 10:43 AM

Hi,

Does anyone know how we can convert a bam file to u ucsc bed file in order to visualize the coverage? I am not a bioinformatician, and tried Galaxy bedtools, but after uploading the converted bed file, I couldnt see the coverage graph but all the NGS reads (huge file). Is there any other easy way to do it with or without galaxy, but without having to program anything?

Thanks
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GenoMax

Senior Member

Join Date: Feb 2008

Posts: 7140
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#2

08-21-2013, 11:10 AM

You may want to use a bedgraph file if you are looking to visualize coverage. That is what you should try to create on galaxy.

I am not sure if you are strictly looking for a utility that has a GUI interface but there are some suggestions in this biostars thread for command line usage: http://www.biostars.org/p/64495/
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