CHOLAR

CHOLAR short for CHaracterization Of LncRNA from rAw Reads).

What does CHOLAR do?

It extracts the list of known and novel lncRNAs from any RNA-seq dataset. As of now, the tool is resticted to human datasets, but we are working hard to include other model organism too.

Installation

For macOS users

brew is a pre-requistic. For information on brew visit https://brew.sh/

Download the zip file for CHOLAR from here or

Download the tar file for CHOLAR from here

After download unzip the file using:

unzip 

For Ubuntu/CentOS users

Download the zip file for CHOLAR from here or

Download the tar file for CHOLAR from here

After download unzip the file using:

unzip

Configuration

Execute the configure file on LINUX/UNIX system using terminal:

bash configure.sh

This will prompt to give password. Enter it and let the script run.

Using CHOLAR

Execute CHOLOAR GUI file using:

bash CHOLAR_GUI.sh

1.1 This will pop up a window to input sample names in the box and sample condition separated by comma.

2.2 Then the Annotation file selection will appear (if it appears daunting, just press ok in both dialog box).

Troubleshoot

Authors

CHOLAR is developed by Haneesh J, Anubha Dey and Manjari Kiran (Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, India).

How to cite CHOLAR

If you use CHOLAR in your publications, you can cite the package as follows:

CHOLAR: Characterization of LncRNA from raw reads.

or in BiBTex:

LICENSE

See the LICENSE file for license rights and limitations.

Acknowledgement

This work is supported by SERB Startup Grant (SRG/2020/002146) from Department of Science and Technology (DST), India.