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 [http://tophat.cbcb.umd.edu/]
* GEM [http://gemlibrary.sourceforge.net]
* SOAPals [http://soap.genomics.org.cn/soapals.html]
So far I am aware of only one program able to display spliced alignments (SeqMonk from http://www.bioinformatics.bbsrc.ac.uk/projects/seqmonk/) but it does not have sequence view.
My question: are there any other programs for next gen spliced mapping visualization? If yes, which input formats they use?
* Tophat [http://tophat.cbcb.umd.edu/]
* GEM [http://gemlibrary.sourceforge.net]
* SOAPals [http://soap.genomics.org.cn/soapals.html]
So far I am aware of only one program able to display spliced alignments (SeqMonk from http://www.bioinformatics.bbsrc.ac.uk/projects/seqmonk/) but it does not have sequence view.
My question: are there any other programs for next gen spliced mapping visualization? If yes, which input formats they use?
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