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
•
written
by
luzglongoria •
1 answer
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).
Log in to answer this question.
-
Mapping transcripts to mitogenome
written by wes •
-
How to make annotation (GFF/GTF) for transcriptome?
written by ahmad mousavi
-
Pathway analyses with a transcriptome, which tool shall I use?
written by luzglongoria •
-
Significance of De Novo Assembly in comparison to Mapping Assembly
written by amansinha.sw •
-
How to combined de novo and genome guided assembly
written by Bioinfonext
-
Mapping of a de novo assembled transcriptome to a genome of relative species
written by seta
-
Finding a Telomere Motif on Streptomyces?
written by ytbyun •
-
Subsetting fasta files based on blast results
written by dpearton •
-
How to add blastx hit name to the related contigs of assembly?
written by sohra •
-
Determining Fpkm Of De Novo Assembly Of Transcriptome
written by James Smith •
I used gmap in the past and it works well .
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.
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.