Thanks kmcarr for your verification 
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Thanks for your explanation in detail, pbluescript
You are very helpful ^^
Do you familiar with "FPKM"?
Based on isoforms.fpkm_tracking and genes.fpkm_tracking, how can I identify whether which transcript or gene is highly expressed, normal, lower expressed in an organism?
For FPKM value, is it I should consider how raw input read (*.fastq) form or assembly as transcript?
I just quite confusing the exact meaning of "Isoform-level relative abundance in Fragments Per Kilobase of exon model per Million mapped fragments".
Can you just show me with a simple example?
Cufflink assembly result only shown those protein-coding transcript, am I right?
It don't shown any non-protein-coding transcript, snRNA, ncRNA,etc, am I right?
Thanks again for advice.Comment
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