FDM User Guide

Overview

FDM tool finds the genes which are differentially transcribed between two samples. It uses alignment information of the short reads from RNA-seq.

Input

  • Alignment files for the reads in SAM format for TWO samples (one or more replicates of the samples)
  • Annotation file in GTF format

     - The definition of GENE start and end coordinates is essential
     - The definition of TRANSCRIPT and EXON is optional

  • List of GENEs for analysis (optional)

Output

  1. FDM results indicating whether the GENEs are differentially transcribed or not, along with a p-value
  2. ACT-Graphs in GFF format

System

FDM is tested to run on Ubuntu 10.04 and up. FDM is written in python.

Installation

Download the tarball from Download page and untar it to a folder, henceforth called fdmroot

Test Run

In following lines, replace fdmroot with complete path per your installation

cd fdmroot/src
./fdm_main.py --config fdmroot/runs/run2600/fdm_2600.cfg

The output will be available in folder fdmroot/report

If you get an error about missing file, you may need to change the following:

In file fdmroot/src/fdmmain.py update the sys.path.append('fdmroot/src') with complete path of fdmroot

Folder Structure

fdmroot
   |----dataout
           |----Sample Name1
                   |----alignment sam file
           |----Sample Name2..n
                   |----alignment sam file
   |----src
           |----fdm source files
   |----runs
           |----config files
   |----report (result files)
           |----FDM_raw
                    |----results files for pair-wise FDM test
           |----result files for replicate FDM test

FDM Run on your data

  1. Place your alignment files in appropriate folders as shown in the above section. You can also look at the  config file fdmroot/runs/run2600/fdm_2600.cfg and use the similar folder structure for your files
  2. Place the annotation file somewhere under fdmroot folder structure.
  3. Create the config file, henceforth called yourconfigfile.cfg
  4. Execute following commands
cd fdmroot/src 
./fdm_main.py --config yourconfigfile.cfg

Creation of config file

Use the config_file_example.txt file available in the tarball as your starting point. All the details of the config file are given in this example file.