I have a set of SRA data (Paired end), for which is it possible to find strand specificity using tools or softwares? And how to identify Antisense RNA and trans-encoded RNA?
You can use RSeQC to estimate whether the library is stranded or not. Antisense RNA is anything on the antisense side, so write a program for it (they probably already exist, but this is a very simple thing to write).
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