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 simply run the program via sirius and follow the prompts. Using the command line flags allows for more customization via flags:

1. -p, --prot string value [Required]

   • 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. The rest of the flags can be defined in any order and are not positional.

2. -n, --num integer value > 2 [Defaults to 2 if unspecified]

   • Specify the number of desired synonymous genes.

3. --hard_rscu_thresh positive floating point value [Defaults to 0.0 if unspecified]

   • 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 [Defaults to this file if unspecified]
       • Path to the .csv file containing amino acid codes, their codons, and the respective RSCU values. The following column names are required: AmOneLet, Codon, and RSCU. No other columns are used; if present, they will be ignored. See this file for an example.

4. -o, --output-folder string value [Defaults to sirius_output if unspecified]

   • SIRIUS will write your results and summary to this folder relative to your current working directory. When an output folder already exists (for example my_output), SIRIUS appends the next available number to this name and creates that folder instead (my_output_1, then my_output_2, and so on). We do not overwrite an existing folder.

5. -q, --quiet no value necessary

   • 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

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Proceed to advanced settings to learn more.