36bp reads will map across splice junctions but at a relatively low rate; you can try changing segment length to get better mapping, but you'll want to evaluate the results carefully to ensure that you're getting good results.
Good luck, J. On Apr 8, 2013, at 5:45 PM, Du, Jianguang wrote: > Hi All, > I have a very basic question. I have RNA-seq datasets of several cell types > and want to compare the alternative splicing events between cell types. The > reads are 36nt in length. Are these reads long enough to map on the splicing > jucntions accurately when I run Tophat with stringent parameters (no > mismatch)? > Thanks. > Best, > Jianguang Du > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
