Usually when I used RSEM I feed my left reads and right reads in as .fastq files. Left is the forward and right is the reverse. I took genome files created an index in STAR and uses quantmode so that I can put the .BAM out file into RSEM.
In the STAR paper it says "--paired-end --forward-prob 0 options are applicable to paired stranded RNA-seq data such as Illumina stranded Tru-seq protocol. Refer to RSEM documentation for detailed description of RSEM parameters."
When I refer to the RSEM manual, it gives this -
---------------- --forward-prob <double> Probability of generating a read from the forward strand of a transcript. Set to 1 for a strand-specific protocol where all (upstream) reads are derived from the forward strand, 0 for a strand-specific protocol where all (upstream) read are derived from the reverse strand, or 0.5 for a non-strand-specific protocol. (Default: 0.5) ----------------------
We used Illumina sequencing, however forward reads are always left and reverse reads are always left.
This has left me confused. Can someone explain this to me kindly?