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Table 1 Parameters of CRISPR screen simulation

From: gscreend: modelling asymmetric count ratios in CRISPR screens to decrease experiment size and improve phenotype detection

Symbol

Variable in software

Default value

Description

Cvirus

cov_virus

400

Coverage during viral transduction.

Ccells

cov_cells

400

Coverage during cell culture.

CPCR

cov_pcr

400

Coverage for PCR amplification.

L

lib_width

7.5

Library distribution width.

Ï„

dupl_time

30

Cell duplication time in hours.

Ï•neg

freq_negfc

0.1

Fraction of gRNAs with negative fitness effect.

Ï•pos

freq_posfc

0.01

Fraction of gRNAs with positive fitness effect.

Ntot

n_sgrnas

50,000

Number of gRNAs in total.

NgRNA

n_sgrnas_per_gene

4

Number of gRNAs per gene.

Nlibpcr

n_repl_lib_pcr

2

Number of replicates for library sequencing.

Nbio

n_repl_sel

10

Number of biological replicates.

Nbiopcr

n_repl_pcr

3

Number of sequencing replicates per biological replicate.

Nsplit

n_splittings

7

Number of cell splittings.

Δt

-

72

Time between cell splittings in hours.