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Old 05-11-2016, 01:23 AM   #6
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

The UCSC file annotations are never that good. The file you downloaded is fine, though again the chromosome names probably differ, which is what's causing problems. I think featureCounts can handle the chromosome naming difference internally, so try using that instead (it's much faster anyway).
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