satay-analysis-laan-lab

This is a first beta version of an automated workflow for processing sequencing data for SAturated Transposon Analysis in Yeast (SATAY).
The main workflow is called satay.sh and is tested in Linux (Ubuntu 20.04). See the readme for the dependencies of this workflow. For more detailed explanation about the dependencies and how to use the workflow, see the documentation.
The final step in the processing is a transposon mapping script that inputs a bam file and outputs an overview of all insertion locations and reads. This can be used independently of the workflow. For this use the transposonmapping_satay.py script.
This release also comes with a number of python scripts that helps analyzing the insertion locations, for example a chromosome-wide and genome-wide overview of the insertion distribution, volcanoplot for comparing fold changes between different strains and a dataframe for easy use of the output data in other python scripts.

• Still lacking automated tests