Function

• Reactivity Calculation calculates the structural reactivity on each nucleotide based on an RT stop count file containing the RT stop count on each nucleotide, typically the output from the Get RT Stop Counts module.

Input:

• 1. RTSC files (Output of Get RT Stop Counts) for (+) and (-) library
• 2. Reference file (fasta) used to map the reads to
• 3. Nucleotide Specificity (Type of nucleotides to have reactivity, e.g. AC for DMS and ACTG for SHAPE)
• [Optional]:
• 1. A threshold to cap the structural reactivities. {Default: 7}
• 2. Flag that determines whether to perform 2%-8% normalization {Default: Yes}

Output:

A text file with structural reactivity for each nucleotide (Reactivity file)