A question about the library preparation for RNA-seq and Directional Strand related settings for RNA-seq Analysis Software The library was prepared was using Clontech Smartseq v4 and Nextera XT So is the library directional and first strand specific (F2R1) or second strand (F1R2)? Which libray type setting should I use for HISAT2, TopHat, Feature Counts etc? Thanks in advance
Regardless of the strandedness of the Clontech Smartseq v4 kit (which I don't know), if you then use the Nextera XT to prepare the final library, I believe it will be unstranded.
Is this the Ultra low input kit?
Yes it is Smartseq v4 Ultra low input kit