I am very new to RNAseq analysis. I have paired end RNAseq data from illumina Hiseq that I aligned using BWA MEM to a virus genome. This generated a BAM file that has alignment flags. I want to distinguish positive strand reads from negative strand as we have RNA from a virus that makes both strands. I have been using the following tags to filter negative and positive reads:
83 and 163 for positive reads 99 and 147 for negative reads
Can someone please confirm if this is correct? Also, how is strandedness determined during library prep. I really struggle to understand this.