Hey all,

I'm trying to map my RADseq to a reference genome, and none of my paired-end reads are being paired. Forward and reverse reads are both mapping separately, but not pairing. This problem is consistent for all of my samples. Any help would be much appreciated!!

I also viewed one of my aligned, sorted, and indexed files in Tablet to visualize where each read pair is being mapped, and most reads are oriented towards each other with ~100 bp in between.

Here is my alignment code with bwa:

bwa mem -M -t 4 -K 10 ./reference_genome.fasta sample1.1.fq.gz sample1.2.fq.gz > mapped.sam

Here's the alignment summary:

279556 + 0 in total (QC-passed reads + QC-failed reads)

86 + 0 secondary

0 + 0 supplementary

0 + 0 duplicates

82256 + 0 mapped (29.42% : N/A)

279470 + 0 paired in sequencing

139735 + 0 read1

139735 + 0 read2

0 + 0 properly paired (0.00% : N/A)

55090 + 0 with itself and mate mapped

27080 + 0 singletons (9.69% : N/A)

29446 + 0 with mate mapped to a different chr

26443 + 0 with mate mapped to a different chr (mapQ>=5)