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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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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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