I suggest you try BBMap - it can map RNA-seq data with very high error rates, including indels, and in my testing greatly outperforms GSNAP. For RNA-seq you have to include a few extra flags from default, as mentioned in that thread.
BBMap as compiled will handle reads up to 500bp. I don't really know how long Ion Torrent reads are so if that's too short, tell me and I can compile it with support for longer reads.
BBMap as compiled will handle reads up to 500bp. I don't really know how long Ion Torrent reads are so if that's too short, tell me and I can compile it with support for longer reads.
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