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dukechem edited this page Nov 14, 2018 · 3 revisions

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 gitlab at https://gitlab.oit.duke.edu in aeh-group area.

== 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. Note: In summer of 2018 Bill Day modified mcff c-source code to add the ability for mcff45 binary to also do all the steps below in one fell swoop. The csv output must be compressed and is too big to open in excel. Work is on hold awaiting response from researchers.

  • "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
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