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In the edgeR analysis, I utilized "total exon reads" as the raw counts. I am wondering if this is fine or not.
Thanks for any comments!
Thanks for any comments!
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What is your biological question of interest ? -
I have two groups. Each group has two subgroups. Each subgroup has 8 replicates. I want to know the differential expression of genes within subgroup, between subgroup and among group.
Thanks!Comment
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You sum the reads in all exons for each gene. That's a good approach. Some experimental protocols also get a lot of intronic reads because many RNAs weren't processed. This avoids that problem. Although it's still possible that in your cell type, the spliced structure of some genes be unannotated and novel. But, counting in exons is the simplest method to use.Comment
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Thank you for the comments!Comment
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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
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