Please note this advice:

You definitely do *not* want to convert BAMs to BEDs.  That would be a step
backwards.  BAM files should display in the genome browser without difficulty,
unless they are attempting to display pile-ups of thousands of reads in the
same location.  In this case you want to use the samtools functions to construct
bigWig pile-up density graphs from your BAM files.

BAM files can display from a URL to your file, you do not need to upload them
to the genome browser.  They are very efficient when used in this manner.


----- Original Message -----
From: "Trent Fowler" <>
Sent: Tuesday, May 29, 2012 11:57:31 AM
Subject: [galaxy-user] Genome Browser Histogram Visualization of Accepted       


I am attempting to run accepted hit data from Tophat output into the UCSC 
Genome Web Browser for visualization of sequencing hits in specific genes. 
However, the BAM files yield tiles and are too large to present through the 
browser. Is there a better file format to convert to that would allow better 
visualization such as histograms? 

>From word of mouth, I have been told to convert BAMs to BEDs and put BED files 
>through the browser. However, I notice that Galaxy does not have an option for 
>this and the oft used BEDtools appears to involve writing code, which is above 
>my computer abilities. 

Any tips or solutions on how to obtain histograms from sequencing data would be 
very welcome. 


Trent Fowler 
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