Map transcripts from de novo assemblier such as trinity back to the genome ?

[sptmbr]

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!

[boetsie]

I would suggest nucmer in the MUMmer package:

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

Very simple and fast.

[kmcarr]

BLAT
GMAP
Exonerate

[jmartin127]

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.

[malachig]

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.

[swaraj]

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)