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Old 08-12-2011, 07:28 AM   #1
sptmbr
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Default Map transcripts from de novo assemblier such as trinity back to the genome ?

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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Old 08-12-2011, 03:41 PM   #2
boetsie
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I would suggest nucmer in the MUMmer package:

http://mummer.sourceforge.net/examples/

Very simple and fast.
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Old 08-12-2011, 05:28 PM   #3
kmcarr
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BLAT
GMAP
Exonerate
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Old 08-12-2011, 09:44 PM   #4
jmartin127
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Quote:
Originally Posted by sptmbr View Post
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!
We usually use Blat for this type of thing. It does a fairly good job.
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Old 08-16-2011, 05:56 AM   #5
malachig
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kmcarr makes some good suggestions.

More options:

Splign
Spidey

If you look at a Refseq record in Genbank, you will notice that 'splign' is the algorithm used by NCBI to determine the exon-intron structure of transcript sequences.
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Old 02-29-2012, 09:47 AM   #6
swaraj
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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)
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