KAS-Analyzer

Overview

KAS-Analyzer is a comprehensive framework for exploring KAS-seq data

KAS-Analyzer is a newly designed, comprehensive methodological framework aimed at simplifying the analysis and interpretation of KAS-seq data. In addition to standard analyses, KAS-Analyzer offers many novel features specifically tailored for KAS-seq data, including, but not limited to: calculation of termination length and index, identification of single-stranded transcribing (SST) enhancers, high-resolution mapping of R-loops, and time-course differential RNA polymerase activity analysis.

KAS-Analyzer is still on active development and the source code is hosted on GitHub.

Restrictions on use

KAS-Analyzer code is licensed under the MIT License and is available on Github.

Set up procedure

We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings.

Load one the following modulefiles:

module load apps/python/kas-analyzer/2.0

Then activate the environment:

source activate /opt/apps/apps/python/kas-analyzer

Running the application

Please do not run KAS-Analyzer on the login node. Jobs should be submitted to the compute nodes via batch.

Serial batch job submission

Create a batch submission script (which will load the modulefile in the jobscript), for example:

#!/bin/bash --login
#$ -cwd             # Job will run from the current directory


# Load the module and activate the environment
module load apps/python/kas-analyzer/2.0
source activate /opt/apps/apps/python/kas-analyzer

KAS-Analyzer download -a bowtie2 -g hg19 -d /path/to/download/directory

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Additional usage info

There is no need for using nohup at the begining and & at the end
as shown in some of the examples in KAS-Analyzer Documentation.

Please do not try to run install and uninstall commands as they will not work.
All necessary tools are already installed and ready to use.

Also, please do not use conda activate KAS-Analyzer,
we use source activate /opt/apps/apps/python/kas-analyzer here instead.

Further info

KAS-Analyzer Documentation
KAS-Analyzer Github

Updates

None.