SEQanswers - View Single Post - Which feature file for htseq-count for non coding elements of ribodepleted samples?

dpryan · 05-11-2016, 01:23 AM

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).

05-11-2016, 01:23 AM	#6
dpryan 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).