I have a strand-specific pair-end Illumina sequencing data. I am not able to understand which option to use in the different software. For each library I have two files: R1 and R2 and I am not sure about forward strand and reverse strand.
I have mapped these R1 and R2 fq files to genome. Please suggest how should I determine which option should I use for Trinity, Hisat2, and StringTie.
Is there any tool to find information about strand-specific pair-end reads?
--SS_lib_type <string> :Strand-specific RNA-Seq read orientation.
if paired: RF or FR,
hISAT2-Paired-end: --fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr)
StringTie --rf assume stranded library fr-firststrand --fr assume stranded library fr-secondstrand