I should be receiving several million PE reads from multiple samples/lanes soon and I am wondering what format the files take.
I know they will be FASTQ but I am wondering do they generally come as one sample per file, one lane per file or something else? Also do the paired ends come in the same or different files?
I plan to align with BWA and it looks like it expects separate files for the paired ends. Is this correct? If samples/lanes/ends need to be separated into individual files, is there a standard way of doing this?
Thanks in advance.