1. Key parameters:
   1. Start/Stop:
      1. “-s”,“—start_codon”,default=”ATG”
      2. “-S”,“—stop_codon”,default=”TAA,TAG,TGA”,
   2. Minimum ORF length
      1. “-m”,“—min-AA-length”,dest=”min_AA_length”,default=”20”
   3. Reads filtering
      1. 5
   4. Specific cutoff
2. 0-based or 1-based
   1. 1-based
   2. ORF_tstart, ORF_tstop: the start and end position of ORF relative to its transcript (1-based coordinate)
   3. ORF_gstart, ORF_gstop: the start and end position of ORF in the genome (1-based coordinate)
   4. pval_frame0_vs_frame1: significance levels of P-site densities of frame0 greater than of frame1
   5. pval_frame0_vs_frame2: significance levels of P-site densities of frame0 greater than of frame2
   6. pval_combined: integrated P-value by combining pval_frame0_vs_frame1 and pval_frame0_vs_frame2
3. ORF type
4. Overlap in annotaion

1. Multiple start codons
   1. “-l”,“—longest-orf”,dest=”longest_orf”,choices=[“yes”,“no”],default=”yes”

The RiboCode generates two text files: The “(output file name).txt” contains the information of all predicted ORFs in each transcript. The “(output file name)_collapsed.txt” file combines the ORFs having the same stop codon in different transcript isoforms: the one harboring the most upstream in-frame ATG will be kept.