GT: Genotyping Comparison Analysis and Clustering/Heatmap

Created: 2011-09-01 17:52:22 Last updated: 2011-09-10 01:01:04

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Creates a genotyping comparison analysis Excel file and heatmap image given final report and gender call input files. User provides a plate number and can choose to either load the data into the database or not (y/n). Note that if user chooses "y" the script will take longer to run.

Before running, make sure the final report and gender call text files are correctly named and that they are in the correct directory under: /gne/research/data/lab-shares/gCell/_gCell/Baseline_Profiling_Cells/Genotyping/Plate_#

Results will be stored under this directory:

/gne/research/data/bioinfo/gcell/genotype/prd/Plate_#

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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (2)

Name	Description
plate_num	[Insert Plate Number]
db_load	[Insert "y" or "n" to indicate whether or not you want to load snp call and gender call data into database for this plate run] *Note that script will take longer to run if you choose "y"

Processors (3)

Name	Type	Description
genotyping_comparison	externaltool
clustering	externaltool
app_dir	stringconstant	Value /gne/research/apps/gcell/prd/arch-indep/bin

Beanshells (0)

Outputs (3)

Name	Description
cluster_status
genotype_status
error_report

Datalinks (9)

Source	Sink
plate_num	genotyping_comparison:plate_num
app_dir:value	genotyping_comparison:app_dir
db_load	genotyping_comparison:db_load
plate_num	clustering:plate_num
app_dir:value	clustering:app_dir
genotyping_comparison:STDERR	error_report
clustering:STDERR	error_report
clustering:STDOUT	cluster_status
genotyping_comparison:STDOUT	genotype_status