Question: cuffdiff long noncoding annotation vs full annotation
gravatar for nand
2.7 years ago by
nand10 wrote:

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.

rna-seq • 770 views
ADD COMMENTlink modified 2.7 years ago by Ben50 • written 2.7 years ago by nand10
gravatar for Ben
2.7 years ago by
Ben50 wrote:

You should align the clean reads to reference genome with the lncRNA gtf, then you can run cuffdiff using the lncRNA gtf

ADD COMMENTlink written 2.7 years ago by Ben50
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