More bug fixes, and a paired-end TopHat tool.

Available here:

See the interface here:

Comments are very welcomed,
Cufflinks is next,

Assaf Gordon wrote, On 03/30/2011 09:21 AM:
> Still very much work-in-progress, but I'd like to hear any comments or ideas 
> that you might have.
> No need to install, just visit here to see TopHat's interface:
> Main differences from the existing TopHat tool:
> 1. Far fewer visible options
> 2. Select "Existing gene mode" (use GTF file) or do De-novo junction 
> detection (or both)
> 3. Allow insertions/deletions detection (with the latest tophat).
> 4. Allow user to specify custom command line parameters.
> 5. Accepts Fasta, FastqSanger, FastqIllumina (but not generic "fastq", per 
> your feedback).
> If you think there are other critical and often used options, let me know.
> updated code is available here:
> -gordon
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