Options to use with inward stranded reverse (ISR) reads

Question

[UserA]

Hi,

I would like to perform a differential gene expression analysis on my dataset. The dataset is made up of paired-end files, and the libraries are ISR type (inward stranded reverse reads). I'd like to be sure that I'm including the right options throughout the analysis for data of this type.

rnaSPAdes :

--ss-rf

Bowtie2-samtools :

**--rf** 

Trinity RSEM :

--SS_lib_type RF

For each step, do I need to note an option indicating that my data are stranded or only for the construction of the metatranscriptome with rnaSPAdes? If I have to indicate it at each step as noted between and are the options the right ones?

Thxs!