2. Tutorial (Basic Settings)

There are two ways to run SIRIUS. The first and simplest is to just call the program and provide i) your protein, and ii) the number of desired sequences, like so ./sirius MALEEINENSTERN -n 6.

The second way is to specify additional parameters via flags as described below.

1. -p, --prot string value

   • The protein flag can be omitted as it is positional. With this flag, you can specify the protein as mentioned above --prot MALEEINENSTERN or -p MALEEINENSTERN or simply omit the flag and just paste your sequence in the second position.

2. -n, --num integer value > 2

   • Specify the number of desired synonymous genes.

3. -h, --hard_rscu_thresh positive floating point value

   • Codons with an RSCU below this value will be completely excluded from the output genes. Using this flag requires you to also specify the following:
     • -c, --codon_usage_fpath string value
       • Path to the .csv file containing amino acid codes, their codons, and the respective RSCU values. The following column names are required: AmOneLet, Codon, RSCU, GC3

4. -q, --quiet

   • Simply supply -q with no value and SIRIUS will not print any logs/errors to the terminal.

A simple execution with flags may look like:

./sirius MALEEINENSTERN -n 3 --hard_rscu_thresh 0.5 --codon_usage_fpath my_codon_usage.csv

Proceed to advanced settings to learn more.