I'm using TopHat, cufflinks, etc. for the first time and am analyzing two small RNAseq datasets, one of which is derived from a RNAi knockdown of a human gene. I tried looking for the relevant gene in the cuffdiff output to validate the experiment and the analysis. For some reason, the gene is not listed (nor are any genomic loci near it). Problem is, I know there were several reads from this gene in both control and knockdown datasets. Am I misunderstanding how TopHat, cufflinks, etc. work and reports results? To me, it looks like the report should contain all hits regardless of whether a significant difference was found or not.
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CRISPR/Cas9 sparked the gene editing revolution for both research and therapeutics.1 But this system still showed severe issues that limited its applications. The most prominent were the heavy reliance on PAM sequences, delivery limitations, double-stranded breaks that prompt unintended edits and cell death, and editing inefficiency (both in targeting and in knock-in reliability).
Despite this, “CRISPR helped turn genome editing from a specialized technique into...07-31-2026, 11:01 AM -
Proteomics platforms are evolving rapidly, with advances in mass spectrometry and affinity-based approaches expanding what researchers can detect and at what scale. As the field moves toward deeper proteome coverage and clinical applications, scientists face an increasingly complex landscape of tools. This article will explore how researchers are navigating these choices to find the right platform for their work.
The systematic characterization of the human proteome has...07-20-2026, 11:48 AM