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Old 05-22-2013, 03:38 PM   #3
Location: Berkeley, CA

Join Date: May 2010
Posts: 50

We do find that we pick up reads that map to lots of these non-coding RNAs, but that they actually throw off the FPKM calculations quite a bit. I remove anything that I don't trust from my GTF file for cufflinks, and that improves the cross-sample reliability quite a bit.
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