mageck2-demo

mageck2-demo stores the demo files for mageck2.

Prerequisite

You will need to install mageck2 in your system first.

How to run the demo

Simply run the script "run.sh" in the respective folder. For example

cd demo1_rra_from_count_table
bash run.sh

Demos

Basic usage of mageck2

• Demo1: Compare two conditions by runing RRA from count table. See the README file on Demo1.
• Demo2: Collect read counts from fastq files, followed by running RRA. See Demo 2.

More functions of mageck2

• Demo3: Compare multiple conditions by using MLE modle, with the option to correct CNV effects. See Demo 3.
• Demo4: Correct CNV effects from RRA. See Demo 4.
• Demo5: Use control guides in RRA or MLE. See Demo 5.

Counting UMIs using mageck2

• Demo6: Count UMIs in fastq file. See the Demo6 for more details.

Counting paired-guide CRISPR screens using mageck2

• Demo7: Count and search for two gRNAs in fastq file. See Demo7 for more details.