Bam to UCSC readable bed file

hdaoud · 08-21-2013, 11:43 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

GenoMax · 08-21-2013, 12:10 PM

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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08-21-2013, 11:43 AM	#1
hdaoud Junior Member Location: Ottawa Join Date: Aug 2013 Posts: 1	Bam to UCSC readable bed file 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

08-21-2013, 12:10 PM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,088	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/