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:
- TopHat
- MapSplice
- SpliceMap
- STAR
- RUM
- GSNAP
- HMMSplicer
- SOAP-splice
- CRAC
- 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:
- How Are Rna-Seq Transcripts Assigned?
- Which Program Should I Test To Map Rnaseq Data? Did Anybody Tried Gsnap?
- Isoform expression quanification from rna seq: flood of tools
- Favorite Splice Site Prediction/Evaluation Tools
- Differentiated expression analysis on isoforms/transcripts level
- Alternative splicing in RNA-Seq
- Novel isoform identification from RNA-seq
- Visualisation Of Alternative Splicing Events Using Rna-Seq Data
- Is There Any Other Method For Isoform-Level Differential Expression Analysis Except Cufflinks/Cuffdiff?
- Best Approach To Predict Novel And Alternative Splicing Events From Rna-Seq Data
- Tools For Visualizing Rna-Seq Splicing Graphs From De Novo Assembly Without A Reference Genome?
- A: Which Program Should I Test To Map Rnaseq Data? Did Anybody Tried Gsnap?
- Has Anyone Tried Rum For Aligning/Counting Illumina Rna-Seq Data?
- Is Tophat The Only Mapper To Consider For Rna-Seq Data?
- Has Anyone Tried Rum For Aligning/Counting Illumina Rna-Seq Data?
•
written
by
amirmhzadeh •
1 answer
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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HSAT aligner from tophat group.
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".
Subjunc -- as fast as STAR.
Segemehl