It seems that the mainstream tools used for RNA-Seq analysis are Tophat and Cufflinks. However, since Tophat is bowtie-based it can't do gapped alignment with short reads. I thought of mapping with BWA and using the resulting SAM with Cufflinks, but as BWA is not meant for RNA-Seq alignment I am hesitant. Does anyone know of an RNA-Seq aligner that supports gapped alignment?
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Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?
Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating...10-14-2026, 09:55 AM -
Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...
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