Ion Torrent Proton RNASeq reads alignment

Question

[mkulecka]

According to this post and poster: https://blog.sbgenomics.com/ion-proton-rna-seq-alignment/ combination of Star and bowtie2 aligners is the best method for RNASeq reads from Proton. However, I am not sure which parameters will be the best for alignment with Star (for bowtie2 the post clearly recommends the default paramteres). Anyone has any experience with this method and can give me some clues?

[Satyajeet Khare]

I am currently analysing Ion Torrent Proton data for RNA-Seq experiment with STAR aligner. But there are quite a few reports using different tools and its a bit confusing. This one, for example finds subJunc or Tophat2 with annotation file better for alignment. This one recommend MaLTA for transcript assembly.

In my initial run I got 68% unique alignment and 7% multi-alignment with STAR with guide GTF file. With soft trimming, however; alignment dropped to 39% which was quite unexpected to me.

Hisat2 alignment without any soft trimming produced 39% unique alignment and 15% multi-alignment. So STAR does look good for my samples.

Answer 1

[WouterDeCoster]

In depth discussion (although I admit that I haven't completely read it - it's in my 'to read' folder) can be found here: http://www.ncbi.nlm.nih.gov/pubmed/27115637

If you can't get access to it... http://sci-hub.cc/