Confused about sambamba syntax for unmapped and mapped
0
0
Entering edit mode
3 months ago
DNAngel ▴ 210

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?

Thank you!

sambamba • 120 views
ADD COMMENT

Login before adding your answer.

Traffic: 785 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6