ggirelli / mud-fish

Melting, Unfolding and Denaturants in Fluorescence In Situ Hybridization (a.k.a. MUD-FISH) allows to identify optimal FISH conditions.

NOTE: the code contained in this repository is just a prototype. It has not been checked for consistency, correctness, or tested against experimental data.

mud-fish

The Melting, Unfolding and Denaturants in FISH (or MUD-FISH) project contains code to select optimal uniFISH 1st and 2nd hybridization conditions for probes composed of oligonucleotides with the following structure: color sequence (C), forward sequence (F), target sequence (T), and reverse sequence (R), from 5' to 3'. Below, I will refer to the longest flap comprising R and C as L (i.e., L=R+C) and to the whole oligo as O (i.e., O=C+F+T+R).

Installation

1. Install OligoArrayAux if not already available. To check if the software is already available run command -v melt.pl or melt.pl --version. The first will give no output if the software is not installed, and the second will show the version of the currently installed software, if any. OligoArrayAux is available here.
2. Install GNU parallel if not already available. To check if the software is already available run command -v parallel or parallel --version. The first will give no output if the software is not installed, and the second will show the version of the currently installed software, if any. GNU parallel is available here.
3. Install datamash if not already available. To check if the software is already available run command -v datamash or datamash --version. The first will give no output if the software is not installed, and the second will show the version of the currently installed software, if any. Datamash is available here.
4. Download fish-conditions repository and submodules.

git clone https://github.com/ggirelli/fish-conditions
cd fish-conditions
git submodule init
git submodule update

5. Test the installation with ./test/test.sh from within the main code folder (e.g., fish-conditions).

For Mac users

Homebrew package manager is needed to install required software. To install homebrew, check out this page.

If not yet available, please install gnu-getopt, parallel, datamash and python3 as follows:

brew install gnu-getopt
brew link --force gnu-getopt

brew install parallel
brew link --force parallel

brew install datamash

brew install python3

Usage

Before starting the analysis, the setting are showed and, after pressing "q", the user has the option to either review the settings again (s), abort the analysis (a) or confirm the settings and start the run (y).

• Consult help page. Run find_fish_conditions.single_probe.sh -h or find_fish_conditions.sh -h for single- or multi-probe manual, respectively.

• Single probe evaluation. Use find_fish_conditions.single_probe.sh -i input.fa -o output_dir/ to run the default parameters over a single probe fasta file.

• Multi-probe evaluation. Use find_fish_conditions.sh -i input.fa -o output_dir/ to run the default parameters over a single probe fasta file.

• Multi-probe harmonization. Use find_fish_conditions.sh -i input.fa -o output_dir/ --harmonize to run the default parameters over a single probe fasta file.

First run

Plot generation is implemented in R and requires the R packages argparse and ggplot2. The script automatically checks for the packages, and tries to automatically install them, providing help in manually installing them if the automatic installation fails.

License

MIT License
Copyright (c) 2017 Gabriele Girelli