One of the rows in my alignment data has the samtool flag of 117.
to figure out what it means. The following is the summary for flag 117:
- read paired
- read unmapped
- read reverse strand
- mate reverse strand
- first in pair
My question is, how could a read be "unmapped" and be "reverse strand(aligned to reference)" at the same time? My guess is samtools define "unmapped" as anything that is not "properly mapped"(meaning both reads in a pair mapped correctly)?