EDIT: I TALKED TO THE REPRESENTATIVE AND SHE EXPLAINED ME THAT THE SMARTER ULTRA LOW + NEXETRA LIBRARIES ARE UNSTRANDED. I GUESS ITS THE SAME FOR FLUIDIGM USING THE SMARTER PROTOCOL. THANKS.
I am little confused with what option to use for rna-stradness when aligning scRNA-seq data. I have two different dataset, one prepared using SMARTer ultralow RNA protocol and second using Fludigm-mRNA seq method. In both method, I see first strand being synthesized first and than the second strand, but as an input for Nextera it suggest the double stranded cDNA is used. Could you help me figure out what rna-stradness opton shall I use for HISAT2:RF (firststrand) or FR?
Fluidigm mRNA seq protocol