BWA does contig orientation matter?

Question

[dp]

I want to find links between contigs in an assembly using paired-end reads. If I'm looking for reads with one end on one contig and the other end on another contig by aligning the reads to the contigs using BWA does the orientation of the contigs matter?

For example if I have contigs C1 and C2 and I map a paired end read such that R_1 maps to C1 and R_2 maps to C2 will I get the same result if I instead used the contig C2' (the reverse complement of C2)?

How does BWA determine the orientation of the paired ends when they map to different contigs?

If in the first case I get the orientation FR for the mapped read pair, then in the second won't I get FF (which isn't considered to be correctly aligned if I understand correctly)?

Answer 1

[swbarnes2]

I don't think that BWA makes any assumptions at all about what the orientation of any of the reads should be with respect to each other, unless maybe it's trying to decide between a few mapping positions. I don't think bwa will refuse to map a read because the contig is one way and not the other.

[dp]

@swbarnes2 Thanks! Do you know if the flags will be set differently in the two cases? If I want to filter (say with samtools) based on the mapping flags, will the FF cases be considered incorrectly mapped?