[galaxy-user] How much can I trimm my reads

Dear All, I am analysing RNA-seq datasets for the differential splicing events between cell types. My reads are 36bp long. In order to increase the quality of reads, I need to trim some nucleotides from ends. How many nucleotides can I trim? I am afraid that if I trim too much, the reliability of the alingment will be affected. Thanks in advance. Jianguang