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Alignment tool for splicing analysis

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.

splicing tophat rna-seq bowtie trinity
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updated by Ram Ram • written by onspotproductions onspotproductions

1 answer

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.

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written by h.mon h.mon

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

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written by cyril-cros cyril-cros

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