When mapping RNA-seq reads to a reference genome, sequences from both directions in the reference are used. To separate the reads in a bam file map to either the forward or reverse strand specifically, we can use the following trick.
samtools view -F 0x10 -h input.bam | samtools view -bS - > forward.bam
samtools view -f 0x10 -h input.bam | samtools view -bS - > forward.bam
Here 0x10 is a flag to indicate whether the reads map to the reverse complement or not.