Question: HISAT2 or Tophat2
0
gravatar for Payal
7 months ago by
Payal20
Payal20 wrote:

Hi I am new to rna seq..I would like to know which one of Tophat2 and Hisat2 is the better aligner for rna-seq data? Or is there an even better option?

rna-seq alignment • 877 views
ADD COMMENTlink modified 7 months ago by Charles Warden4.8k • written 7 months ago by Payal20
1

Between those two, HISAT2 is the latest so you would want to use that.

ADD REPLYlink written 7 months ago by genomax32k
9
gravatar for poisonAlien
7 months ago by
poisonAlien2.4k
Asgard
poisonAlien2.4k wrote:

Simulation-based comprehensive benchmarking of RNA-seq aligners

One should definitely read this and decide themselves.

Spoiler: Dont use tophat!

The most widely cited tool underperforms for most metrics, particularly when using default settings.

ADD COMMENTlink modified 7 months ago • written 7 months ago by poisonAlien2.4k
2

I have to give you an upvote because Tophat is so terrible, but so used.

ADD REPLYlink written 7 months ago by Brian Bushnell13k
1

Another thing that should be considered is how robust the results are to different parameters. In the Baruzzo study, almost all the aligners could be configured to give good results, but they differed in the performance of the default options, with STAR looking pretty good in those terms. I have to say though, we use HISAT a lot just because of how easy it is and how few resources it requires.

ADD REPLYlink written 7 months ago by i.sudbery1.4k

That paper has "some" issues, just don't read the conclusion, be very critical on their method. For example, they used the beta version of HISAT2 and not the latest.

ADD REPLYlink written 7 months ago by WouterDeCoster20k

Agreed. Regardless, above conclusion wouldn't have changed IMO.

ADD REPLYlink written 7 months ago by poisonAlien2.4k
3
gravatar for Brian Bushnell
7 months ago by
Walnut Creek, USA
Brian Bushnell13k wrote:

I think BBMap and STAR are better options, and TopHat is generally not very good. I wrote BBMap; it's very accurate and indexes very quickly. STAR uses slightly more memory but is quite a bit faster.

However, this kind of question will spawn a lot of differing opinions.

ADD COMMENTlink written 7 months ago by Brian Bushnell13k
3
gravatar for Geparada
7 months ago by
Geparada1.2k
Cambridge
Geparada1.2k wrote:

1.-Do not use Tophat2. Nowadays you have many much better options, just look a the bechmarks.

2.- STAR it is pretty good, I would totally recommend it. However the issue with STAR is the high memory requirement. If you are working with human and you have less than 28 GB of RAM memory, you should use HISAT2 instead. Otherwise, both aligners programs should perform very similar.

ADD COMMENTlink written 7 months ago by Geparada1.2k
3
gravatar for Charles Warden
7 months ago by
Charles Warden4.8k
Duarte, CA
Charles Warden4.8k wrote:

I would say it depends on what you want to do with your data.

I've sometimes found that the TopHat alignments work better than STAR alignments with some splicing analysis programs, possibly due to the format of the alignment.

I would consider the run-time for TopHat to be sufficiently quick that you could run comparisons and see what works best with your data (while the benchmark papers can be a useful starting point, the optimal strategy is not necessarily the same for every dataset). So, if the combination of latest aligner and downstream algorithm gives results that don't make sense, it may be a good idea to try other aligners / algorithms.

There are also options for gene expression quantification without the alignment step (Salmon, kallisto, Sailfish, etc.). If you have a two-group comparison with triplicates and clear expression differences, then that should work fine. However, I've found the accuracy for gene assignments for a given sample may be less accurate, and having replicates can give you some sense in the robustness of the read / expression assignments for transcripts (or the sum of transcripts for genes).

ADD COMMENTlink written 7 months ago by Charles Warden4.8k
2
gravatar for WouterDeCoster
7 months ago by
Belgium
WouterDeCoster20k wrote:

I would suggest STAR, or maybe, if it fits your needs, alignment-free methods such as kallisto and salmon.

ADD COMMENTlink written 7 months ago by WouterDeCoster20k
0
gravatar for Payal
7 months ago by
Payal20
Payal20 wrote:

Thank you for all your suggestions.

ADD COMMENTlink written 7 months ago by Payal20
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