Hello, I am trying to save the complete header lines in my Fasta file using BWA. Once I've mapped the reads to the references genome and I want to extract the ones that mapped and output them to a fasta file. I need the reads to have the complete header name they originally had.
After looking for a while I see the option: bwa mem -R ’@RG\tID:foo\tSM:bar’. The problem is I don't understand this string i need to input and I get an error every time I try to use it. I know the above string is just an example, but I would be very grateful if some could explain this. Or propose a different way to output the complete header line for the reads from bwa. Thanks