iontorrent RNAseq alignment

Question

[kanwarjag]

What aligner may be best for ion torrent RNA-seq data; I generally use for illumina TopHat. Any pointers please.

[Brian Bushnell]

I suggest you try BBMap, as it is capable of handling both splice junctions and the Ion Torrent's indel-containing error profile. Are you aligning to a genome or transcriptome, and what species?

[kanwarjag]

I am aligning to hg19 genome. That mean we cannot use TopHat for ion torrent. I could not find exact paper but I remember they have used top Hat and unaligned reads were realigned with Bowtie2 both TopHat and Bowtie2 alignments combined and used for differential analysis. Any thoughts. Otherwise I can turn to BBMap

Thanks

[Brian Bushnell]

You can try TopHat + Bowtie2, or just TopHat alone. They should work, but I would expect BBMap to be faster and do a better job. For human genome RNA-seq alignment I recommend adding the flags "maxindel=100k intronlen=10".