A method of processing an RNA sample is provided. In certain embodiments, the method may comprise: a) obtaining a fragmented RNA sample comprising: i. RNA fragments of long RNA molecules; and ii. unfragmented short RNA; and b) contacting said fragmented RNA sample with a first adaptor in the presence of a RtcB ligase, thereby producing a ligated RNA sample comprising adaptor-ligated fragments of long RNA. A kit for performing the method is also provided.