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Welcome to the Rna-fold-lab-scripts wiki!

== Description ==

This "Rna-fold-lab-scripts" project analyzes MC-Flashfold output for randomized RNA seq inputs. The code is kept on github at https://github.com/dukechem/Rna-fold-lab-scripts

== Prerequisites ==

• python3 on mac-os-x or Linux.

• MC-Flashfold software. Download MC-Flashfold-v34.zip version 3.4 (May 2015) from Major's lab and follow included pdf instructions to setup to run on Linux or Macintosh osx.

== General Protocol ==

The procedure has the following scripts run from command line script(s), with output (stdout) from each step piped to input of next step (stdin).

• "Run" SeqGen
• "Run" mcff (MC-FlashFold) for generated seqs
• "Run" sort-seq.py
• "Run" cps.py to generate final results as csv file (comma seperated values) that opens in excel, gnumeric, etc

== To Do yet ==

• Filter 2D structures to keep only those who have all of the "static" base pairs computed previously
• Generate color-coded 2D representations to identify the statistics