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Old 12-14-2011, 06:35 AM   #4
Alex Renwick
Location: Houston, Texas

Join Date: Jul 2011
Posts: 44

Does IGV show any error message?

Be sure you're using the sorted.bam file. IGV will find the associated index file from the name and ".bai" extension, but it won't go looking for the sorted file if you give an unsorted one.

One possibility is that you need to zoom in. At the whole genome level nothing is shown. The data doesn't show up until the window is zoomed so that the window spans less than 50kb.
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