I got a bunch of Illumina lanes from RNA-Seq experiment and corresponding draft genome sequence. There are few alignment programs I can use which can handle splicing:
- Tophat (works, requires filtering short reads from fastq)
- GEM (works, tabulated output, some manual output combining required)
- SOAPals (works on example data, genome indexing fails on my input)
So far I am aware of only one program able to display spliced alignments (SeqMonk) but have not managed to run it yet.
My question: are there any other programs for next gen spliced mapping visualization? If yes, which input formats they use?
EDIT: One more new tool for spliced mapping:
See also thread on SeqAnswers
SpliceMap works on test data, strange format of input reads.