GPP Web Portal - Analyze CRISPR-based screening data

Clone Pool: Select a CP# from the dropdown if one has been assigned. If not, provide a custom chip file in the proper format by loading one below.

Strict Strict sequence match to NCBI genes (PREFERRED) Lax Lax sequence match to NCBI genes

Chip File: Upload a custom chip file in the following format: .txt file with the first column listing individual sgRNAs in the pool, and column two listing the gene identifier for the sgRNA target in the first column.

Total # guides:

Average # guides/gene:

Total # one-intergenic-site control guides These guides each have one (and only one) perfectly scoring match to an intergenic site :

Total # no-site control guides These guides have no perfectly scoring match to the genome :

Data File: Screen data in the following format: .txt file with the first column listing the sgRNAs as specified in the first column of the asssociated chip file and consecutive columns listing the numerical inputs for each condition provided in the screen.

Directionality Of Scores: Select "Positive" if the best perturbation has the highest/most positvie value (enrichment) and "Negative" if the best perturbation has the lowest/most negative value (depletion). Use "Both" if you want the screen to be analyzed in both directions.

Both Positive Negative

Threshold %: A number ranging from 0 - 100. This indicates the x% of sgRNAs for which a STARS score will be calculated. A value of 10 is standard but can be specified based on the signal in the particular biological assay.

Include first barcode in calculation: Specify whether the first ranking perturbation for each gene should be used in the calculation of STARS score.

Yes No

Top n% guides per gene: The n% guides per gene to be used in the calculation of average p-value and average log-fold change. The default value is 100% which uses all guides per gene to calculate average p-value and average log-fold change.

Must be between 1 and 100

Create negative control "dummy" genes w/ n guides per gene: Number of control guides to be used to create "dummy" control genes. Average number of guides per gene in the library is the suggested value.

Must be an integer - typically similar to # guides per gene

Display Parameters

# of genes to label: The number of genes to be labeled on the enrichment and depletion side of the resulting volcano plot.

Must be an integer less than or equal to 6; recommend 3-5

Min # of guides required per gene: Minimum number of guides required for a gene to be plotted on the resulting volcano plot.

Must be an integer that is smaller than the maximum # of guides

Max # of guides required per gene: Maximum number of guides required for a gene to be plotted on the resulting volcano plot.

Must be an integer that is greater than the minimum # of guides

Display no-site controls: Include no-site controls on the resulting volcano plot.

Display one-intergenic-site controls: Include one-intergenic-site controls on the resulting volcano plot.

New Analysis for CRISPR-based Screening Data

Display Parameters