More bug fixes, and a paired-end TopHat tool.
Available here: http://cancan.cshl.edu/labmembers/gordon/files/cshl_rnaseq_2011_04_04.tar.bz...
See the interface here: http://cancan.cshl.edu/publicgalaxy/root?tool_id=cshl_tophat_pe1
Comments are very welcomed, Cufflinks is next, -gordon
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: http://cancan.cshl.edu/publicgalaxy/root?tool_id=cshl_tophat_se1
Main differences from the existing TopHat tool:
- Far fewer visible options
- Select "Existing gene mode" (use GTF file) or do De-novo junction detection (or both)
- Allow insertions/deletions detection (with the latest tophat).
- Allow user to specify custom command line parameters.
- 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: http://cancan.cshl.edu/labmembers/gordon/files/cshl_rnaseq_tools_1.tar.bz2
-gordon