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Next-Gen Sequencing tools from the Horvath Lab

RNA2DNAlign Installation

RNA2DNAlign is available in two forms, a self-contained packaged binary for 64-bit Linux systems, and as Python source. We recommend the self-contained packaged binary for Linux systems.

RNA2DNAlign for 64-bit Linux

Unpack the downloaded release:

 tar xzf RNA2DNAlign-*.tgz
 ln -s RNA2DNAlign-* RNA2DNAlign

The RNA2DNAlign program is located in the bin subdirectory:

 ./RNA2DNAlign/bin/RNA2DNAlign -h
    
 ./RNA2DNAlign/bin/RNA2DNAlign 

Test the install using the provided example data:

 cd RNA2DNAlign
 ./bin/RNA2DNAlign -r "data/example-*.bam" -s "data/example-SNV.tsv" -o testing

Python 2.7 RNA2DNAlign

Unpack the downloaded release:

 tar xzf RNA2DNAlign-*.tgz
 ln -s RNA2DNAlign-* RNA2DNAlign

Locate your Python binary and ensure it is version 2.7:
```
 python --version

 /path/to/python2.7 --version 
```
We refer to the Python binary as python below, please substitute whatever path and version numbers are required to run Python 2.7 on your system. We recommend the Enthought Python Distribution (EPD) which pre-installs all but the pysam third-party dependencies needed by RNA2DNAlign.
Ensure the necessary third-party Python modules are installed. pysam version >= 0.8.1 is required.
```
 pysam, numpy, scipy
```
For the configuration and execution GUI (optional):
```
 wx
```
For Excel format SNV input files (optional):
```
 xlrd, openpyxl
```
The existence of required modules can be tested as follows (demonstrated here for scipy):
```
 python2.7 -c "from scipy import __version__; print __version__"
```

The RNA2DNAlign program is located in the src subdirectory:

 python ./RNA2DNAlign/src/RNA2DNAlign.py -h
    
 python ./RNA2DNAlign/src/RNA2DNAlign.py

Test the installation using the provided example data:

 cd RNA2DNAlign
 python ./src/RNA2DNAlign.py -r "data/example-*.bam" -s "data/example-SNV.tsv" -o testing

RNA2DNAlign Installation

RNA2DNAlign for 64-bit Linux

Python 2.7 RNA2DNAlign

See Also