Low Pairing of R1 and R2

[seqome]

Hi Guys,

It happened with only 1 sample, For others it was all good.

Pairing was low 10.99%. Normally for other samples, I am getting around 80%. What could go wrong with it.

The pipeline was BWA-MEM with default parameters + samtools. rna 2*150bp

Below is the output from flagstat


SAM tools FlagStat
AB612
2394946 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
37488 + 0 supplementary
0 + 0 duplicates
2366833 + 0 mapped (98.83% : N/A)
2357458 + 0 paired in sequencing
1178729 + 0 read1
1178729 + 0 read2
259168 + 0 properly paired (10.99% : N/A)
2320108 + 0 with itself and mate mapped
9237 + 0 singletons (0.39% : N/A)
58364 + 0 with mate mapped to a different chr
5947 + 0 with mate mapped to a different chr (mapQ>=5)

[GenoMax]

Have you checked to make sure that your input sequence files are in sync as far as R1/R2 go. You can use `repair.sh` from BBMap suite to bring them in sync if they are not (e.g. if mates are missing from one or both files).