Mapping transcripts to genome

Question

[luzglongoria]

Hi,

I have done a de novo transcriptome assembly, now I'm trying to map the assembled transcriptome to a genome of relative species. I have been reading about which program should I use. What do you think about using BBMap, Spaln or GMAP ? Which one fit better with this kind of analyses?

Thanks,

Luz

[Nicolas Rosewick]

I used gmap in the past and it works well .

[h.mon]

Spaln2 and GMAP were developed to map, among other things, cDNA to a genome, so they are appropriate. Exonerate also is appropriate, and minimap2 probably will work very well for this task.

[Juke34]

This paper could be of interest Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln that incorporates additional species-specific features Unfortunately BBMap was not existing at the time of this review.

Answer 1

[Charles Warden]

I think I had to change some parameters (and also have manual review of the annotation) to get a reasonable result. However, if your goal is genome annotation, perhaps you can see if MAKER can help?

This can use de novo predictions in addition to RNA-Seq data (I think that was primarily through results like a cufflinks genome-guided assembly, but you could also try treated the assembled transcripts like ESTs and/or comparing the effect of using a genome-guided assembly).

[Juke34]

MAKER use blastx+ exonerate to map the proteins to the genome.