Spliced aligners for RNA-seq
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5.9 years ago
amirmhzadeh ▴ 80

Hello,

I'm working on RNA-Seq data. I am planing to evlaute the performance of the below-listed RNA-seq spliced aligners to find the most befitting one for my study. It is worth mentioning that the species of my interest is homo sapiens.

Right now I am considering the following aligners:

  1. TopHat
  2. MapSplice
  3. SpliceMap
  4. STAR
  5. RUM
  6. GSNAP
  7. HMMSplicer
  8. SOAP-splice
  9. CRAC
  10. QPALMA

I know this question has been asked repeatedly over the past few years and there are many great and thorough answers for it but I am wondering if there are some RNA-seq splice aligners out there that I have never heard of?

Any advise would be greatly apprecited.

Cheers,

-A

P.S. I am including some relevant posts from BioStar and SeqAnswers here for future references by the readers:

RNA-Seq alignment next-gen • 3.1k views
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HSAT aligner from tophat group. 

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BBMap

Here's a nice poster of it:

http://1ofdmq2n8tc36m6i46scovo2e.wpengine.netdna-cdn.com/wp-content/uploads/2013/11/BB_User-Meeting-2014-poster-FINAL.pdf

The defaults are fine for organisms with short introns<16kbp.  For vertebrates or other organisms with very long introns be sure to set "maxindel=200000".

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Subjunc -- as fast as STAR.

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5.9 years ago
h.mon 32k

Unless you want to write a paper comparing spliced aligners, I would read the literature relevant for your area and pick two or three aligners for testing. Are you willing to optimize parameters for each program, or just use defaults? A program performing badly may just need some tuning.

All in all, it seems just an enormous amount of work, to probably get a small improvement (I am speaking from experience).

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