I'm looking for a bit of a history lesson. Its been a while since I've seen this, but I recall that there was a time when fastq files (or qseqs) contained dots in place of uncalled bases where now there will be an 'N'.
Does anyone know when the transition was made?
Also, can most major aligners handle both '.' and 'N' in place of an uncallable base?
Some aligners I'm interested in:
Any information on the topic would be helpful.