Reference file for seq.error

Hi everybody,

I’ve done MiSeq tutorial and I’ve a question about seq.error command.
Reference file for seq.error is always HMP_MOCK.v35.fasta or it depends of my data?


It depends on what you used for your mock community. You would need to use the reference sequences for the bacteria in your mock community. And of course, if you didn’t use a mock community in your sequencing, you wouldn’t run seq.error.