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I was wondering if some one has used Top hat aligned RNA-seq reads to quantify differential expression cf noncoding RNA between case and control samples.
Thanks
Thanks
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I haven't used it, but i guess it should not be any different, in comparison to coding genes. As long as RNASeq captures ncRNA expression, the use of tophat and cufflink should be able to tell you the use of differential expression. However, the lower expression (in general) level of ncRNA, might not give the better picture of differential expression, unless you have a very high coverage.
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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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