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You can, but that is an entirely different question to should you. There was actually a very good post about this 3 days ago which you can view here
Ironically, don't have the heart to mark a question about duplicates as a duplicate of a question about duplicates, but if you feel that the other post answers your question, you should consider moderating yourself :)
Hello ash!
There are many many threads already discussed about duplicates and RNA-Seq.
Should We Remove Duplicated Reads In Rna-Seq ?
Duplicated Reads In Rna-Seq Experiment
http://seqanswers.com/forums/showthread.php?t=6854
Given that your data is single-end, its not recommended to remove duplicates. Please read the discussions in above posts.
For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.
If you disagree please tell us why in a reply below, we'll be happy to talk about it.
Cheers!