Analysis scripts for lnrCXCR4 lncRNA paper
The analysis was performed on a ubuntu 16.04 workstation with 32 cores. Adjust the value of NUMPROC
variable to match the number of cores in your machine.
These can be installed either system-wide or in user space. Make sure the appropriate executables are on PATH
.
Create the virtual environment and install python dependencies like so:
$ pyvenv ~/.venv/RNAcapture
$ source ~/.venv/RNAcapture/bin/activate
(RNAcapture)$ pip install -r requirements.txt
The analysis is organized into three jupyter
notebooks:
Download the reference, extract appropriate sequences and build the index for bowtie2
Perform quality trimming and reads alignment to the reference. Prepare locus coverage files for the next step.
Plot the coverage of the reference locus along with provided .gtf
annotations
To run the analysis download the data files and place them in the top level RNAcapture
directory:
|-RNAcapture
|---data
| |---yoon01
| |---yoon02
| |---yoon03
...
Then activate RNAcapture
environment and launch jupyter
:
$ source ~/.venv/RNAcapture/bin/activate
(RNAcapture)$ jupyter notebook