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Thank you very much for your website and all of your help. I am attempting to use IGV to look at a few genes in order to calculate the number of non-synonymous SNPs. However, there were large regions where the number of reads dropped from 10000 to as low as 500. If we find that there is a region with a high rate of nonsynonymous SNPs but it only contains an average of 500 reads at that point is that significant if other regions contain 5000 reads? In other words, if a single nucleotide shows 5% variability (eg 95% A and 5%T) with 500 reads is that similar to 5% variability at 5000 reads? Or do we need to treat the 4500 reads not showing up in IGV at that spot as potentially too dissimilar to run statistical analysis? Any help or references you could provide would be much appreciated.
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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...Yesterday, 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 -
With the launch of new single-cell sequencing platforms in 2026, the field stands at an exciting inflection point. This article surveys the most impactful advances in the field and discusses how they’re reshaping research in cancer, immunology, and beyond.
Introduction
Single-cell sequencing technologies have undergone remarkable advances over the past decade, transitioning from low-throughput experimental approaches to highly scalable platforms capable of...05-22-2026, 06:42 AM