I was using Cufflinks to analyze Clip-Seq data. The results as 'gene
expression' and 'transcript expression' gave me almost same results (No. of
genes ? No. of transcripts). I guess the number of genes should be
relatively smaller than that in transcripts.  I wonder if I need to get a
special format for the annotation? I used '62: UCSC Main on Human: refGene
(genome)'.

 

Thanks,

Songyan Liu

 

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