PRE-PROCESSING

[Rita Domingues]

I am trying to improve the --fastq_filter option and have two questions:

(1) Should I choose --fastq_maxee_rate or --fastq_maxee?
(2) What is the difference between --fastq_trunclen and --fastq_minlen?

[Colin J Brislawn]

Hello!

Hopefully you have found the answers already, but if not, here's how I would address these.

(1) Should I choose --fastq_maxee_rate or --fastq_maxee?

Because most amplicon sequences are a constant length, these are equivalent. For example, with 250 bp reads maxee_rate = 0.02 is the same as  maxee = 5, because 5 errors / 250 == 2% error rate.

For variable length reads, you will have to choose if you want to bias / select for longer reads. Because longer reads have more bases, they will have a greater total EE.

(2) What is the difference between --fastq_trunclen and --fastq_minlen?

trunclen will TRUNCate the reads at a given LENgth, cutting off their ends.

minlen will discard / remove reads from the output if they are shorter than a given MINimum LENgth.

Colin