GT: Genotyping Comparison Analysis and Clustering/Heatmap
Created: 2011-09-01 17:52:22
Last updated: 2011-09-10 01:01:04
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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Authors (1)
![header=[] body=[These are the descriptive titles embedded within the workflow version] cssheader=[boxoverTooltipHeader] cssbody=[boxoverTooltipBody] delay=[200] Information](/images/famfamfam_silk/information.png?1680607579)
Titles (1)
GT: Genotyping Comparison Analysis and Clustering/Heatmap |
![header=[] body=[These are the descriptions embedded within the workflow version] cssheader=[boxoverTooltipHeader] cssbody=[boxoverTooltipBody] delay=[200] Information](/images/famfamfam_silk/information.png?1680607579)
Descriptions (1)
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_# |
![header=[] body=[These are the listed dependencies of the workflow] cssheader=[boxoverTooltipHeader] cssbody=[boxoverTooltipBody] delay=[200] Information](/images/famfamfam_silk/information.png?1680607579)
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 |
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 |
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