How to properly combine two bam files of a paired-end data

Hi all!

I am mapping a paired-end read separately using bowtie2.

After that, I want to combine the two bam file into one for downstream analysis.

How to properly do this combination?

I tried:

samtools sort -n R1.bam R1.sorted
samtools sort -n R1.bam R1.sorted
samtools merge R1_R2.bam R1.sorted.bam R2.sorted.bam

But it seems not working. The header of the R1_R2.bam is like following:

603889264 + 0 in total (QC-passed reads + QC-failed reads)

0 + 0 duplicates

590620124 + 0 mapped (97.80%:-nan%)

0 + 0 paired in sequencing

0 + 0 read1

0 + 0 read2

0 + 0 properly paired (-nan%:-nan%)

0 + 0 with itself and mate mapped

0 + 0 singletons (-nan%:-nan%)

0 + 0 with mate mapped to a different chr

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

Which shows that the alignment of R1 and R2 are no properly paired. Also there is no @RG header line in the combined file.

What might be the problem?

Thanks a lot!!!