I've found various ways to change the notation of the chromosomes in my bam files. However, would it be a bad idea to add my sample identifier to the chromosome notation? For example, changing chrX to chrX_US1 for the first US sample. I have a large data set and I'm going to be running analyses per chromosome, so I'm worried once I start I won't be able to determine which chromosome came from where.
Prior to making my sorted consensus sequences, all the samples were mapped with the same reference genome so shouldn't need to be realigned. Instead, I'm just going to move them all those I'm comparing into the same .fasta file.
I am very new to this, so could be making huge mistakes, hence asking on here.
Thanks in advance.