I am trying to align my paired-end reads to my assembly with bwa mem (to be used for polishing with Racon afterwards). However due to downstream application requirements (Racon) my paired-end reads have to have the same ID, which bwa does not accept on its paired-end mode. So in order to use all my reads I treated my paired-end reads as single reads for alignment with bwa mem (by deleting the ID content after the space in the header line '@' and merging both fastq files).
Now I am wondering if this approach I took was a good call or not? If so what would be the problematic here? How significant would be the difference in the quality of the alignment treated this way vs properly as paired-end? Can this alignment cause a spurious polishing later when using Racon?
I would appreciate much to have your thoughts. Thanks!