Hello,

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.

Thanks

Trent Fowler