Best way to align RNA unaligned .ubam files from Ion Torrent

Question

[genya35]

Hello,

Could someone please suggest a good way to align an unaligned Ion Torrent .ubam files containing RNA reads, so we could identify the breakpoints in IGV?

Thanks

Answer 1

[genya35]

Could you please suggest a pipeline for aligning RNA fastQ files, bam being the final output?