I have used STAR to map my reads to hg19. I was wondering how a read, which is complementary to the reference genome, gets aligned to the reference? I assume the software will automatically generate the complementary strand of the reference, and map the reads to the correct position, but how I could know whether the read has the same sequence as the reference itself or its complementary strand?
Another question is about "samtools mpileup". I am doing a Illumina paired-end RNA-seq, and the sequencing results contain read 1 and read 2. If I see a dot, does it mean there is a read (either from read 1 or read 2) map to the reference; or a read 1 map to reference (maybe the reference genome itself or its complementary)? Same question for the common. Does it mean a read (either read1 or read 2) map to the reference; or one read from read 1 map to the the reference sequence or its complementary? I will appreciate any help!