TransExtract Beta version 1.2

Extract Transitions from PARCLIP data. This is beta version, this could be improved by including more description about the results and also with graphical visualization.

Prerequisites: (For getting output as graphs)

Installed R version 2.0 or greater

Input VCF must be Version 4.0 (Output from tool Freebayes)

Execute/Run script:

1. Unzip the TransExtract_betaV1.2.zip folder and go into the extracted folder.

2. Edit 'TransExtract.sh' file. The comments with two hashes '##' means the input must be provided.

3. Edit 'run_config.sh' file. The comments with two hashes '##' means the input must be provided.

4. chmod a+x *.pl

5. chmod a+x *.sh

6. ./TransExtract.sh

Scripts workflow:

output from Freebayes (Input) --> accessTransition.pl --> Transitions_extraction.pl --> run_config.sh --> TransExtract.sh

INPUT: This supports VCF file from Freebayes (https://github.com/ekg/freebayes) or Other programs.

Conclusion from the run:

Outcome in Publication: Figure 1c from " Mondal et. al, 2015. MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA–DNA triplex structures. Nature Communications (Scripts used for this publication)".