Description

mageck count for functional genomics, reads are usually mapped to a specific sgRNA

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

inputfile:file

library fastq file containing the sgRNA and gene name or count table containing the sgRNA and number of reads to per sample

*.{fq,fastq,fastq.gz,fq.gz,csv,txt,tsv}

library:file

library file containing the sgRNA and gene name

*.{csv,txt,tsv}

Output

name:type
description
pattern

count

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*count.txt:file

File containing read counts

*.countsummary.txt

norm

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.count_normalized.txt:file

File containing normalized read counts

*.count_normalized.txt

versions

versions.yml:file

File containing software versions

versions.yml

Tools

mageck
BSD License

MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout), an algorithm to process, QC, analyze and visualize CRISPR screening data.

sourceforge.net/p/mageck/wiki/Home sourceforge.net/p/mageck/wiki/demo/#step-4-run-the-mageck-count-command 10.1186/s13059-014-0554-4
crisprseq
Github user LaurenceKuhl
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