Question: Alignment tool for splicing analysis
gravatar for onspotproductions
3.4 years ago by
United States
onspotproductions130 wrote:

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. 

ADD COMMENTlink modified 3.4 years ago by h.mon24k • written 3.4 years ago by onspotproductions130
gravatar for h.mon
3.4 years ago by
h.mon24k wrote:

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.

ADD COMMENTlink written 3.4 years ago by h.mon24k

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

ADD REPLYlink written 3.4 years ago by cyril-cros890
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