Hello, 

I was wondering if anyone determined a method to compare two alignment methods? 

I created a pipeline similar to the UCSC pipeline and i wanted to compare my 
results with that of another researcher's lab created alignment. I am unsure 
how exactly they created their files, but they are also in multiple alignment 
format. 

Thank you for any assistance or advice.

Guillermo Monroy
Undergraduate Researcher
Univ. of Il @ Urbana Champaign

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