Why different rna-seq aligners need to be used for Ion Torrent data compared with illumina?

Question

[Vasu]

The aligners used for illumina RNA-seq data were Tophat, Hisat2, Star etc.. I see that for Ion Torrent RNA-Seq data there are different aligners like TMap and BBMap.

Tophat, Hisat2, Star can also be used for Ion Torrent RNA-Seq data?

Are there any other aligners for Ion Torrent RNA-Seq data? And Why cant we use Tophat, Hisat2 or Star for Ion torrent RNA-Seq data?

What are the differences between Mira/BBMap and Tophat/Hisat2/Star?

[Titus]

Hi, Where did you get this information ? I think the major differences concern the handling of low complexity region which are source of error in Torrent sequencing.

Best

[GenoMax]

Before we go too far, can you confirm what kind of Ion data are you referring to? Someone (hopefully not you) had recently mixed RNAseq with AmpliSeq on Ion Torrent over at SeqAnswers.

[Vasu]

I have Ion Torrent RNA-Seq data. In Seqanswers the guy was talking about Ampliseq I guess.

[GenoMax]

My comments there should be applicable in this case then. Curious to know where you got some of the info in your original question.

[Vasu]

I see here a guy was asking similar question - [iontorrent RNAseq alignment] Some where I saw that people were saying that tophat, hisat2 cant be used for Ion torrent Rna-seq data and they were telling to use BBMap/ TMap etc

Answer 1

[h.mon]

Because Illumina and Ion Torrent are different technologies, and their reads have different error profiles. See a previous discussion here, in addition to the other links provided in the comments above.

P.S.: it is not you can't use the same aligners, but the optimal settings will probably differ, and the defaults for each aligner are optimized for a particular error profile.

[Vasu]

Thank you. I saw that just few mins back. I understood now from your comment in this post ion torrent alignment software