Alignment tool for splicing analysis

Question

[onspotproductions]

I am currently doing splicing analysis on some RNA-seq data and created a de novo assembly for use in analysis through trinity. I would like to know whether bowtie or tophat is the better choice for aligning the reads back to the trinity reference file. I have used tophat previously for alignment for expression analysis, but am unsure which would provide more useful/cleaner output data about splice junctions.

Answer 1

[h.mon]

You have to read the paper to get a full picture, as depending on the situation the best mapper may change, but:

In general, GSNAP, GSTRUCT, MapSplice and STAR compared favorably to the other methods, [...]

STAR is really fast, I don't know about the others.

[cyril-cros]

STAR stores a lot of data in RAM. If you have access to good hardware, it is lightning fast.