Envision Screen data cleaning

Author: Sam Lee, samleenz@me.com

Date: 2017-12-05

Yeast screen initial analysis pipeline. From a set of paired 384 well plates find the wells that exhibit the greatest growth defects across plate pairs for further analysis and potential follow-up.

The code was written with a certain setup in mind from an Envision screen so while it is generalisable there will likely be some changes required e.g. for exclusion of control wells and ensuring mapping of well numbers to alpha-numeric coordinates is correct.

Directory strucutre

• code/ has the scripts for processing
• data/ contains raw data files
• results/deltas has the delta files for each plate in /data
• results/z-score has ranked z-score lists for each plate and a plot of the z-score distribution for each plate in z-score/plots
• results/paired-hits are the lists of plate coordinates where z-score < -2 for the duplicate plates
• results/summary.txt is the summary file for the pipeline. It lists each pair and the number of "hits" in descending order.

Deltas

• Deltas (differences) are calcualted as the difference between every well ij, for i rows and j columns, and the arithmetic mean of column 23 and 24.
• The filenames for the deltas match the raw filename but with the addition of _delta to the end of each file.

Z-score

• The Z-score is a centred transformation of the delta values where they are moved from an absolute scale to the standard deviation scale
• columns [1,2,23,24] (controls) are removed prior to the z-score transformation so do not affect the distribution of the standard deviations
• The filenames for the z-scores match the raw filename but with the addition of _zscore to the end of each file.

Configuring the Snakemake pipeline

To configure the pipeline for execution the plate name pairs must be specified in the config.yaml file as follows:

pairs:
    A: SCW0137251_084229_003___SCW0137252_084229_002
    B: SCW0137253_084229_001___SCW0137254_084229_004

The triple-underscore ___ betwen the plate names is important.

To test the pipeline once the config file is edited use

snakemake --dag --forceall | dot -Tpng > dag.png
#or
snakemake -npr

To execute:

snakemake

If further plate pairs are added only those that have not been run will be re-calculated if snakemake is called again.

misc

To regenerate this readme from the markdown doc:

pandoc -s README.md -o README.html