MAGeCK Count Report
Author: Wei Li, weililab.org
Parameters
comparison_name is the prefix of your output file, defined by the “-n” parameter in your “mageck test” command. The system will look for the following files to generate this report:
- comparison_name.countsummary.txt
- comparison_name.count_normalized.txt
- comparison_name.log
# define the comparison_name here; for example,
# comparison_name='demo'
comparison_name='cdh1'Preprocessing
Reading input files. If any of these files are problematic, an error message will be shown below.
cstable=read.table(count_summary_file,header = T,as.is = T)
nc_table=read.table(normalized_cnt_file,header = T,as.is = T)Summary
The summary of the count command is as follows.
| File | Label | Reads | Mapped | Percentage | TotalsgRNAs | Zerocounts | GiniIndex |
|---|---|---|---|---|---|---|---|
| /juno/work/solitlab/jc/Project_11252_D/trimmed/CDH1hi.merged.fastq.gz | High | 16112919 | 4105474 | 0.2548 | 77438 | 3324 | 0.17500 |
| /juno/work/solitlab/jc/Project_11252_D/trimmed/CDH1lo.merged.fastq.gz | Low | 18839795 | 5681368 | 0.3016 | 77438 | 3007 | 0.16920 |
| /juno/work/solitlab/jc/Project_11252_D/trimmed/Lib.merged.fastq.gz | CTRL | 43856292 | 40320961 | 0.9194 | 77438 | 40 | 0.05808 |
The meanings of the columns are as follows.
- File: The filename of fastq file;
- Label: Assigned label;
- Reads: The total read count in the fastq file;
- Mapped: Reads that can be mapped to gRNA library;
- Percentage: The percentage of mapped reads;
- TotalsgRNAs: The number of sgRNAs in the library;
- ZeroCounts: The number of sgRNA with 0 read counts;
- GiniIndex: The Gini Index of the read count distribution. Gini index can be used to measure the evenness of the read counts, and a smaller value means a more even distribution of the read counts.
If –day0label and –gmt-file options are provided, the following metrics will display the degree of negative selections of essential genes (provided by –gmt-file).
| File | Label | NegSelQC | NegSelQCPval | NegSelQCPvalPermutation | NegSelQCPvalPermutationFDR | NegSelQCGene |
|---|---|---|---|---|---|---|
| /juno/work/solitlab/jc/Project_11252_D/trimmed/CDH1hi.merged.fastq.gz | High | 0 | 1 | 1 | 1 | 0 |
| /juno/work/solitlab/jc/Project_11252_D/trimmed/CDH1lo.merged.fastq.gz | Low | 0 | 1 | 1 | 1 | 0 |
| /juno/work/solitlab/jc/Project_11252_D/trimmed/Lib.merged.fastq.gz | CTRL | 0 | 1 | 1 | 1 | 0 |
The meanings of the columns are as follows.
- NegSelQC: the enrichment score (ES) of essential genes in the negative selection list. The score is calculated using GSEA;
- NegSelQCPval: the associated p value of the enrichment score;
- NegSelQCPvalPermutation: the permutated p value of the enrichment score;
- NegSelQCPvalPermutationFDR: the adjusted permutated p value;
- NegSelQCGene: the number of genes used for the analysis.
Normalized read count distribution of all samples
The following figure shows the distribution of median-normalized read counts in all samples.
The following figure shows the histogram of median-normalized read counts in all samples.
Principle Component Analysis
The following figure shows the first 2 principle components (PCs) from the Principle Component Analysis (PCA), and the percentage of variances explained by the top PCs.
The variance of the PCs
Sample clustering
The following figure shows the sample clustering result.
