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
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