Strand Specific mapping

[ionescu]

Hi

I would like to do strand specific mapping to a set of bacterial RNA-Seq files. The libraries were prepared using the KAPA hyperprep kit and should "by definition" be strand specific. I used bbmap for mapping (a tool I often use) but the result, as viewd in Artemis suggests there is no strand specific data i.e. both strands are nearly mirror one of the other.

Before assuming the sequencing center did something wrong - I would like to be sure I am doing the mapping correctly.

can someone please advise on the parameters for BBMAP (or another tool if needed) to obtain strand specific mapping.

Thanks