Just need some clarification on the logic here.
If I want all unmapped reads, would I use "unmapped AND mate_is_unmapped" or would I use "unmapped OR mate_is_unmapped". LIkewise, if I want all mapped reads, I would use "not (unmapped AND mate_is_unmapped)" or "not (unmapped OR mate_is_unmapped)". I would think I would need to use "OR" so that it meets either condition, but sources online have been using "AND".
I just want to ensure I am getting two separate bamfiles. One with all unmapped reads and one with all mapped reads. Syntax is confusing me a bit. Is the "AND" treating the two conditions as separate options, almost like if I wrote them as two separate lines, or is it treating the two conditions that both have to be met by a read for it to be extracted?