Hi all, 

I have two small RNA libraries that are biological replicates. I mapped 
the reads onto the genome using Bowtie and displayed the BAM files as 
two individual tracks on the UCSC genome browser. However, this is not 
very nice.

Ideally, I would like to color the reads from each library with a 
different color, so that I could display them in the SAME track. Because
 the two replicates are color labeled, I would be able to tell which 
experiment a particular read comes from. 

I have two BAM files from each library. All I need to do is to label 
them with different colors, then merge them before displaying on genome 

Does anyone know how to do this? 

Thanks in advance for your help!

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