According to the Bowtie2 manual, Bowtie2 writes the reverse complement sequence of the original read into the SAM file output if the read maps to the reverse complement of the reference (--> negative strand, FLAG = 16).
Cited from the manual:
10. Read sequence (reverse-complemented if aligned to the reverse strand)
What happens in the local alignment mode ? I can't find a description for that. Is the output also reverse-complement ? For the whole read sequence ? Or only for the mapped part ?
From my data I would say it is not reverse complement.
Thank you for your help/experience.