Q1. I came across above representations here on seqanswers. What do these two scenarios tell us about paired end library preparation. Is the 2nd one corresponding to "reversely" stranded scenario - like in the case of Agilent SureSelect RNA-Seq capture protocol? This is for me to have a clear understanding in my head.
Q2. Are there any transformations (reverse complementing) that Aligners do to these original reads sequences when they create a SAM/BAM file? I understand there are certain binary flags that are meant to say whether the reads are paired end, what strand the read is on, if the read is first or second in the paired end case,etc. Is there also a flag to say whether the sequence is reverse complement or it's original - is the strand information corrected accordingly? How do aligners take a decision on when to transform?
Thank you, for clearing away my confusion.