Question: Mapping transcripts to genome
0
gravatar for luzglongoria
3 months ago by
luzglongoria20
luzglongoria20 wrote:

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

rna-seq assembly gene • 248 views
ADD COMMENTlink modified 3 months ago by Charles Warden6.6k • written 3 months ago by luzglongoria20
3

I used gmap in the past and it works well .

ADD REPLYlink written 3 months ago by Nicolas Rosewick7.5k
1

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.

ADD REPLYlink modified 3 months ago • written 3 months ago by h.mon24k
1

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.

ADD REPLYlink written 3 months ago by Juke-342.1k
0
gravatar for Charles Warden
3 months ago by
Charles Warden6.6k
Duarte, CA
Charles Warden6.6k wrote:

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).

ADD COMMENTlink modified 3 months ago • written 3 months ago by Charles Warden6.6k

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

ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by Juke-342.1k
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