liulab-dfci/mageck

Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.

mageck's Issues

Need some help to learn tool

Hello everyone,
I am here in search of help to know the tool mageck better a s I am facing problem in allignling my reads on library file. ZerosgRNA is having 0 count. Can you help me in this??

Do I have to trim off all other bases but only keep guide RNA sequences in the raw data before applying MAGeCK?

Hi,

Gene Renaming bug

Hi,

When using MLE,

All gene names which start with "SG" e.g. SGSH, SGPP1, SGPP2, SGMSH are truncated to remove the SG in the negsg.mle.gene_summary.txt and subsequent files, while in the counts, these genes have their complete names as part of the guides e.g. sgSGPP2_9.

This leads into downstream analysis bugs when doing GSEA, ORA or any other tools needs to recognise the gene e.g. transcript/ protein mapping.

This doens't actually change the hits themselves and wasn't too extensive. In my library, only 5/3000 genes started with "SG" but this really depends on the library used.

Thanks