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MALTA: a calculator for estimating the coverage with shRNA, CRISPR, and cDNA libraries
Journal article   Open access   Peer reviewed

MALTA: a calculator for estimating the coverage with shRNA, CRISPR, and cDNA libraries

Venkatramanan Krishnamani, Mark A. Stamnes and Robert C. Piper
SoftwareX, Vol.9, pp.154-160
01/01/2019
DOI: 10.1016/j.softx.2019.01.006
PMCID: PMC6625779
PMID: 31304228
url
https://doi.org/10.1016/j.softx.2019.01.006View
Published (Version of record) Open Access

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Abstract

Genetic screens using shRNA, CRISPR, or cDNA libraries rely on adequately transferring the library into cells for further assay. These libraries can have many different elements and each element can be present at different copy numbers within a given pooled library. Calculating how many recipient cells are needed to adequately sample all or most of the different elements within a library is important, especially if one wants to compare the outcomes of different genetic screens that rely on accurately reproducing the starting population of library-containing cells. Here we present a simple application that starts with a list of library elements and their abundance and calculates the minimum sampling number to achieve full transfer of the library to an acceptor cell population to a user-specified level of probability. Users can adjust several input parameters including designating a subpopulation over which the calculation is made. Finally, the program performs a series of Monte Carlo simulations of a user-specified number of picks to produce an empirically determined distribution of each library element.
 Computation Genetic Screening pooled libraries

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