De Novo Assembly And Comparative Genomics

Question

[ascendo.u]

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.

Answer 1

[Haibao Tang]

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.