Recent changes to output

output modified by Wei Li

Wei Li — Thu, 17 Mar 2022 01:58:27 -0000

--- v30
+++ v31
@@ -84,7 +84,11 @@
 FDR | false discovery rate    
 high_in_treatment | Whether the abundance is higher in treatment samples

-
+## sgrna_summary_txt in mle subcommand ##
+
+Note that this file will have different meaning in mle subcommand: it records the estimated efficiency probability of the guides in the MLE model, after the termination of iteration. 
+
+Note that by default, this value is 1 since --sgrna-efficiency is turned off. The values will be between 0-1 if you turn this option on and/or if you explicitly set up the --sgrna-efficiency parameter.  

 ## gene_summary_txt ##

output modified by Wei Li

Wei Li — Fri, 02 Jul 2021 18:25:39 -0000

--- v29
+++ v30
@@ -15,6 +15,7 @@
 * [.gene.high.txt](#gene_txt):  The gene ranking results (positively selected genes).
 * [.gene.low.txt](#gene_txt):   The gene ranking results (negatively selected genes).

+The following files are the inputs of RRA and will be deleted after MAGeCK is complete.

 ## count_summary_txt##

@@ -190,7 +191,27 @@
 lo_value  | The raw p-value      
 FDR | The false discovery rate

-
+### RRA input ###
+
+
+An example of the sgrna ranking file (.plow.txt or ..phigh.txt) is as follows. These files are the input of RRA.
+
+    sgrna   symbol  pool    p.low   prob    chosen
+    Drug_0009853    TOP2A   list    -31.3383375285032       1       1
+    Drug_0010808    RPS11   list    -29.865960506388134     1       1
+
+
+The contents of each column is as follows.
+
+
+Column | Content
+-------|---------
+sgrna   | sgRNA ID     
+symbol | Gene ID        
+pool  | Depreciated column. Set all the values in this column as a single value (e.g., "list")    
+p.low | The score used to sort sgRNA (increasing order)
+prob|Reserved column. Set to 1
+chosen|Reserved column. Set to 1


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output modified by Wei Li

Wei Li — Fri, 02 Jul 2021 18:18:35 -0000

--- v28
+++ v29
@@ -10,7 +10,7 @@
 * [pathway_summary.txt](#pathway_summary_txt): The pathway ranking results.
 * [log](#log): The logging information during the running.

-Other file formats are intermediate files, including:
+The following files are the outputs of RRA. They are intermediate files and are deleted after MAGeCK running is complete. To see these files, use the *--keep-tmp* option in MAGeCK test subcommand.

 * [.gene.high.txt](#gene_txt):  The gene ranking results (positively selected genes).
 * [.gene.low.txt](#gene_txt):   The gene ranking results (negatively selected genes).

output modified by Wei Li

Wei Li — Wed, 11 Nov 2020 21:42:31 -0000

--- v27
+++ v28
@@ -71,8 +71,8 @@
 Gene | The targeting gene 
 control_count | Normalized read counts in control samples  
 treatment_count | Normalized read counts in treatment samples 
-control_mean  | Mean read counts in control samples  
-treat_mean  | Mean read counts in treatment samples    
+control_mean  | Median read counts in control samples  
+treat_mean  | Median read counts in treatment samples    
 LFC | The log2 fold change of sgRNA
 control_var | The raw variance in control samples    
 adj_var | The adjusted variance in control samples

output modified by Wei Li

Wei Li — Fri, 07 Dec 2018 16:28:53 -0000

--- v26
+++ v27
@@ -109,9 +109,8 @@
 neg|rank | The ranking of this gene in negative selection
 neg|goodsgrna | The number of "good" sgRNAs, i.e., sgRNAs whose ranking is below the alpha cutoff (determined by the [--gene-test-fdr-threshold](http://sourceforge.net/p/mageck/wiki/usage/#test) option), in negative selection.
 neg|lfc | The log2 fold change of this gene in negative selection. The way to calculate gene lfc is controlled by the [ --gene-lfc-method](http://sourceforge.net/p/mageck/wiki/usage/#test) option
-pos|score| The number of targeting sgRNAs for each gene in positive selection (usually the same as num.neg)      
-pos|score | The RRA lo value of this gene in negative selection  
-pos|p-value  | The raw p-value of this gene in positive selection    
+pos|score | The RRA lo value of this gene in positive selection  
+pos|p-value  | The raw p-value (using permutation) of this gene in positive selection    
 pos|fdr | The false discovery rate of this gene in positive selection
 pos|rank | The ranking of this gene in positive selection
 pos|goodsgrna | The number of "good" sgRNAs, i.e., sgRNAs whose ranking is below the alpha cutoff (determined by the [--gene-test-fdr-threshold](http://sourceforge.net/p/mageck/wiki/usage/#test) option), in positive selection.

output modified by Wei Li

Wei Li — Tue, 10 Jul 2018 18:43:06 -0000

--- v25
+++ v26
@@ -73,7 +73,7 @@
 treatment_count | Normalized read counts in treatment samples 
 control_mean  | Mean read counts in control samples  
 treat_mean  | Mean read counts in treatment samples    
-LFC | The log fold change of sgRNA
+LFC | The log2 fold change of sgRNA
 control_var | The raw variance in control samples    
 adj_var | The adjusted variance in control samples 
 score | The score of this sgRNA
@@ -108,7 +108,7 @@
 neg|fdr | The false discovery rate of this gene in negative selection
 neg|rank | The ranking of this gene in negative selection
 neg|goodsgrna | The number of "good" sgRNAs, i.e., sgRNAs whose ranking is below the alpha cutoff (determined by the [--gene-test-fdr-threshold](http://sourceforge.net/p/mageck/wiki/usage/#test) option), in negative selection.
-neg|lfc | The log fold change of this gene in negative selection
+neg|lfc | The log2 fold change of this gene in negative selection. The way to calculate gene lfc is controlled by the [ --gene-lfc-method](http://sourceforge.net/p/mageck/wiki/usage/#test) option
 pos|score| The number of targeting sgRNAs for each gene in positive selection (usually the same as num.neg)      
 pos|score | The RRA lo value of this gene in negative selection  
 pos|p-value  | The raw p-value of this gene in positive selection

output modified by Wei Li

Wei Li — Thu, 10 May 2018 17:40:51 -0000

--- v24
+++ v25
@@ -137,6 +137,7 @@
 HL60|beta;KBM7|beta | The beta scores of this gene in conditions "HL60" and "KBM7", respectively. The conditions are specified in the design matrix as an input of the mle subcommand.        
 HL60|p-value  | The raw p-value (using permutation) of this gene    
 HL60|fdr | The false discovery rate of this gene 
+HL60|z | The z-score associated with Wald test
 HL60|wald-p-value | The p value using Wald test
 HL60|wald-fdr | The false discovery rate of the Wald test

output modified by Wei Li

Wei Li — Tue, 16 Jan 2018 19:24:22 -0000

--- v23
+++ v24
@@ -27,18 +27,18 @@
     S5_R1_001.fastq.gz LNCaP_Day0  16659017    14497805    0.8703  92817   461 0.0996  0   1   1   1   0.0

-The contents of each column are as follows.
+The contents of each column are as follows. **To help you evaluate the quality of the data, recommended values are shown in bold.**

 Column | Content
 -------|---------
-File|The fastq (or the count table) file used
-Label|The label of that fastq file assigned
-Reads|Total number reads in the fastq file
+File|The fastq (or the count table) file used.
+Label|The label of that fastq file assigned.
+Reads|Total number reads in the fastq file. **(Recommended: 100~300 times the number of sgRNAs)**
 Mapped|Total number of reads that can be mapped to library
-Percentage|Mapped percentage, calculated as Mapped/Reads
+Percentage|Mapped percentage, calculated as Mapped/Reads **(Recommended: at least 60%)**
 TotalsgRNAs|Total number of sgRNAs in the library
-Zerocounts|Total number of missing sgRNAs (sgRNAs that have 0 counts)
-GiniIndex|The [Gini Index](https://en.wikipedia.org/wiki/Gini_coefficient) of the read count distribution. A smaller value indicates more eveness of the count distribution.
+Zerocounts|Total number of missing sgRNAs (sgRNAs that have 0 counts) **(Recommended:  no more than 1%)**
+GiniIndex|The [Gini Index](https://en.wikipedia.org/wiki/Gini_coefficient) of the read count distribution. A smaller value indicates more eveness of the count distribution. **(Recommended: around 0.1 for plasmid or initial state samples, and around 0.2-0.3 for negative selection samples )**

 The following column is used to evaluate the degree of negative selection in known essential genes. It is set only if you provide the --day0-label option. MAGeCK will run pathway analysis for each sample, and use several GSEA metrics to evaluate the quality of the samples.

@@ -46,7 +46,7 @@
 Column | Content
 -------|---------
 NegSelQC|The Enrichment Score (ES) of GSEA 
-NegSelQCPval|The p value of the GSEA analysis  
+NegSelQCPval|The p value of the GSEA analysis  **(Recommended: smaller than 1e-10)**
 NegSelQCPvalPermutation|The permutation p value
 NegSelQCPvalPermutationFDR|The FDR of the permutation p value  
 NegSelQCGene|The number of essential genes found in the library that are evaluated for GSEA analysis.

output modified by Wei Li

Wei Li — Tue, 16 Jan 2018 19:12:35 -0000

--- v22
+++ v23
@@ -4,6 +4,7 @@

 The output of the MAGeCK consists of the following files:

+* [countsummary.txt](#count_summary_txt): Count summary and QC measurements.
 * [sgrna_summary.txt](#sgrna_summary_txt): The sgRNA ranking results.
 * [gene_summary.txt](#gene_summary_txt): The gene ranking results.
 * [pathway_summary.txt](#pathway_summary_txt): The pathway ranking results.
@@ -13,6 +14,43 @@

 * [.gene.high.txt](#gene_txt):  The gene ranking results (positively selected genes).
 * [.gene.low.txt](#gene_txt):   The gene ranking results (negatively selected genes).
+
+
+## count_summary_txt##
+
+This file is generated by count command, and summarizes QC measurements of the fastq (or count table) files.
+
+An example is as follows:
+
+    File   Label   Reads   Mapped  Percentage  TotalsgRNAs Zerocounts  GiniIndex   NegSelQC    NegSelQCPval    NegSelQCPvalPermutation NegSelQCPvalPermutationFDR  NegSelQCGene
+    S6_R1_001.fastq.gz LNCaP_Day21 15567122    13033442    0.8372  92817   2204    0.1472  0.68965 1.6688e-31  0   0   86
+    S5_R1_001.fastq.gz LNCaP_Day0  16659017    14497805    0.8703  92817   461 0.0996  0   1   1   1   0.0
+
+
+The contents of each column are as follows.
+
+Column | Content
+-------|---------
+File|The fastq (or the count table) file used
+Label|The label of that fastq file assigned
+Reads|Total number reads in the fastq file
+Mapped|Total number of reads that can be mapped to library
+Percentage|Mapped percentage, calculated as Mapped/Reads
+TotalsgRNAs|Total number of sgRNAs in the library
+Zerocounts|Total number of missing sgRNAs (sgRNAs that have 0 counts)
+GiniIndex|The [Gini Index](https://en.wikipedia.org/wiki/Gini_coefficient) of the read count distribution. A smaller value indicates more eveness of the count distribution.
+
+The following column is used to evaluate the degree of negative selection in known essential genes. It is set only if you provide the --day0-label option. MAGeCK will run pathway analysis for each sample, and use several GSEA metrics to evaluate the quality of the samples.
+
+
+Column | Content
+-------|---------
+NegSelQC|The Enrichment Score (ES) of GSEA 
+NegSelQCPval|The p value of the GSEA analysis  
+NegSelQCPvalPermutation|The permutation p value
+NegSelQCPvalPermutationFDR|The FDR of the permutation p value  
+NegSelQCGene|The number of essential genes found in the library that are evaluated for GSEA analysis.
+

 ## sgrna_summary_txt ##

output modified by Wei Li

Wei Li — Fri, 02 Dec 2016 17:48:37 -0000

--- v21
+++ v22
@@ -53,10 +53,10 @@

 An example of the gene summary file is as follows:

-    id      num     neg|score  neg|p-value   neg|fdr neg|rank        neg|goodsgrna   pos|score  pos|p-value   pos|fdr pos|rank  pos|goodsgrna
-    ESPL1   12      6.4327e-10      7.558e-06       7.9e-05 1       11      0.99725 0.99981 0.999992        615     0
-    RPL18   12      6.4671e-10      7.558e-06       7.9e-05 2       11      0.99799 0.99989 0.999992        620     0
-    CDK1    12      2.6439e-09      7.558e-06       7.9e-05 3       12      1.0     0.99999 0.999992        655     0
+    id      num     neg|score  neg|p-value   neg|fdr neg|rank        neg|goodsgrna    neg|lfc   pos|score  pos|p-value   pos|fdr pos|rank  pos|goodsgrna    pos|lfc
+    ESPL1   12      6.4327e-10      7.558e-06       7.9e-05 1    -2.35    11      0.99725 0.99981 0.999992        615     0    -0.07
+    RPL18   12      6.4671e-10      7.558e-06       7.9e-05 2    -2.12    11      0.99799 0.99989 0.999992        620     0    -0.32
+    CDK1    12      2.6439e-09      7.558e-06       7.9e-05 3    -1.93    12      1.0     0.99999 0.999992        655     0    -0.12

 The contents of each column is as follows.

@@ -70,12 +70,14 @@
 neg|fdr | The false discovery rate of this gene in negative selection
 neg|rank | The ranking of this gene in negative selection
 neg|goodsgrna | The number of "good" sgRNAs, i.e., sgRNAs whose ranking is below the alpha cutoff (determined by the [--gene-test-fdr-threshold](http://sourceforge.net/p/mageck/wiki/usage/#test) option), in negative selection.
+neg|lfc | The log fold change of this gene in negative selection
 pos|score| The number of targeting sgRNAs for each gene in positive selection (usually the same as num.neg)      
 pos|score | The RRA lo value of this gene in negative selection  
 pos|p-value  | The raw p-value of this gene in positive selection    
 pos|fdr | The false discovery rate of this gene in positive selection
 pos|rank | The ranking of this gene in positive selection
 pos|goodsgrna | The number of "good" sgRNAs, i.e., sgRNAs whose ranking is below the alpha cutoff (determined by the [--gene-test-fdr-threshold](http://sourceforge.net/p/mageck/wiki/usage/#test) option), in positive selection.
+pos|lfc | The log fold change of this gene in positive selection

 Genes are ranked by the p.neg field (by default). If you need a ranking by the p.pos, you can use the --sort-criteria option.