Pierre gives a good suggestion.
Merging will most likely result in incorrect values that affect things such as stranding and which read belongs to which, in later analysis. These SAM flags will become incorrect unless they will be 'fixed' on top of a merge:
- read paired (0x1)
- read mapped in proper pair (0x2)
- mate unmapped (0x8)
- read reverse strand (0x10)
- mate reverse strand (0x20)
- first in pair (0x40)
- second in pair (0x80)
The same accounts for the RNEXT and PNEXT fields.
A remap will solve all these issues. Good luck!
Youri
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