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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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Genomics studies in neuroscience face a special challenge due to the brain’s complexity and scarcity of samples. Mapping changes in cell type and state using conventional next-generation sequencing methods remains challenging. Advances in technologies like single-cell sequencing, spatial transcriptomics, and long-read sequencing have opened the door to deeper studies of the brain and diseases like Alzheimer’s, amyotrophic lateral sclerosis (ALS), and schizophrenia.
...07-09-2026, 11:10 AM -
Cancer survival rates have significantly increased in the last few decades in the United States, reaching a combined 70% 5-year survival rate by 2021. Behind this number, there are years of research to find new therapies, drug targets, and early detection methods. But there is one core challenge that keeps slowing down these advances, and it’s about drug resistance.
There is no single reason why many patients don’t respond to treatment as expected. Cancer is...07-08-2026, 05:17 AM -
Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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