cuffdiff long noncoding annotation vs full annotation
I'm studying differential expression of long non coding RNA. Should I run cuffdiff using the gencode annotation file with all transcripts, and then filter out lncRNA data, or run cuffdiff with annotation of only long noncoding RNAs? If I use full transcripts annotation, FPKM values are much lower than that with only lncRNA transcripts. I prefer to use lncRNA annotation because it gives about ten times more significant transcripts.
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