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Old 10-04-2017, 02:23 PM   #2
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Location: Florida

Join Date: Oct 2017
Posts: 3

I have answered my own question, but I am posting just in case someone else has a similar issue.

I ran the same tophat data with stringtie and got a similarly bad correlation between technical replicates of 0.62. Now I know that the problem must be with stringtie and not with hisat2.
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