eco32i / RNAcapture

Analysis scripts for lnrCXCR4 lncRNA paper

RNAcapture

Analysis scripts for lnrCXCR4 lncRNA paper

Dependencies

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.

Non-python dependencies

These can be installed either system-wide or in user space. Make sure the appropriate executables are on PATH.

• samtools v1.5.2
• bedtools v2.26
• bowtie2 v2.3.0
• Trimmomatic

Python dependencies

Create the virtual environment and install python dependencies like so:

$ pyvenv ~/.venv/RNAcapture
$ source ~/.venv/RNAcapture/bin/activate
(RNAcapture)$ pip install -r requirements.txt

Running notebooks

The analysis is organized into three jupyter notebooks:

00 - Build reference.ipynb

Download the reference, extract appropriate sequences and build the index for bowtie2

01 - Quality trimming and alignment.ipynb

Perform quality trimming and reads alignment to the reference. Prepare locus coverage files for the next step.

02 - Locus coverage plots.ipynb

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