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Hi, could anyone recommend any software or algorithm to map the transcripts generated from de novo assembly algorithm such as trinity back to the reference genome? Thanks in advance!
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I would suggest nucmer in the MUMmer package:
Very simple and fast. -
We usually use Blat for this type of thing. It does a fairly good job.Originally posted by sptmbr View PostComment
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blastn -query query.fa -db db -out query.backmapped -num_threads 4 -culling_limit 1 (for same species)
blastn -query query.fa -db db -out query.backmapped -num_threads 4 -culling_limit 1 -task blastn(for different species)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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