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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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