If I have a strand-specific paired-end library and align with Tophat with an option like fr-firstrand
, what is the proper to encode the strand of the pairs in the BAM, and how do mappers like Tophat handle it? With fr-firstrand
we know that the first strand is the strand of the read, but by definition the second mate will be on opposite orientation. If the first read in the pair has strand +
in its alignment in the BAM file, then will the second read in the pair also have strand +
or can we count on it being -
? Thanks