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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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Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...04-04-2024, 04:25 PM -
Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...03-22-2024, 06:39 AM
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