Question: De Novo Assembly And Comparative Genomics
gravatar for ascendo.u
7.4 years ago by
United States
ascendo.u10 wrote:

Hi all,

I am trying to do comparative genomics with a plant RNA-seq data (no genome available).

I have assembled the short reads with trinity

After this, I try to align this short read to other reference genome which has similar genome.

Is there any suggestion for this comparative genomics aligntment tool?

Any advice would be very much appreciated. Thank you in advance.

next-gen rna-seq • 1.7k views
ADD COMMENTlink modified 7.1 years ago by Haibao Tang3.0k • written 7.4 years ago by ascendo.u10
gravatar for Haibao Tang
7.4 years ago by
Haibao Tang3.0k
Mountain View, CA
Haibao Tang3.0k wrote:

Align your Trinity transcripts, not individual reads, to the related genome is your best bet. It is unclear how close your species is to related references, but they might have good amounts of DNA substitutions in between. Therefore you need an alignment tool that is more sensitive. Popular choices for aligning transcripts to genomes are: exonerate, gmap, sim4/sim4cc, and BLAT.

ADD COMMENTlink written 7.4 years ago by Haibao Tang3.0k
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