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Old 07-15-2014, 01:01 AM   #1
StevenVanLaere
Junior Member
 
Location: Belgium

Join Date: Jun 2014
Posts: 3
Unhappy 0% Concordant Pair Alignment Rate

Dear all,

After aligning a paired-end library to the reference genome using TopHat2 with settings: inner mate distance = 0, standard deviation inner mate distance = 200 (based on the traces profile), I can't find any concordantly aligned pair. Is this normal?

Thanks,

Steven
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