fastx_learn command

See also
unoise3 command

Determines error rates of amplicon reads. Input is a set of unique sequences with size=annotations . The input file is usually generated by the fastx_uniques command with the -sizeout option. It can be in FASTQ or FASTA format. If FASTQ format is provided, then the expected errors predicted by the Q scores are compared with the measured error rates, and the accuracy of the Q scores is measured by comparing the observed and predicted error rate for each value of Q. Click here for an example report .

This command is useful for checking the error rate after expected error quality filtering , which assumes that the Q scores are accurate. It does not use Q scores so gives an indpendent check.

The -output option specifies a text file to contain the report.

Example

usearch -fastx_learn uniques.fastq -output learn.txt