I have a multiplexed lane of GBS sequencing reads as a fastq file. I understand the first step is to demultiplex and trim the adapter sequences from the reads.
This yields many individual fastq files that correspond to individual libraries.
My question is how should I perform the BWA MEM alignment?
Do I perform BWA MEM on each of the resulting fastq files that correspond to individual libraries...
Should I perform BWA MEM on the large original fastq file that contains all my sequence reads before demux and read trimming?
Forgive my ignorance, I've only ever used TASSEL (which works great) and I'm trying to expand my understanding and flexibility.