PinAPL-Py
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**************************************************
Launching PinAPL-Py v2.8.1
P. Spahn et al., UC San Diego (11/2017)
**************************************************


**************************************************
Running character sanity check ...
**************************************************
No special characters found.
Character sanity check completed.




**************************************************
Reading data ...
**************************************************
Found sample Control_1
Found sample Control_2
Found sample ToxA_1
Found sample ToxA_2
Found sample ToxB_1
Found sample ToxB_2

Data input completed.




**************************************************
Running sequence quality control ...
**************************************************
Started analysis of Control_R2_S15_L008_R1_001_x.fastq.gz
Approx 5% complete for Control_R2_S15_L008_R1_001_x.fastq.gz
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Analysis complete for Control_R2_S15_L008_R1_001_x.fastq.gz
Started analysis of ToxB_R1_98_S4_L008_R1_001_x.fastq.gz
Approx 5% complete for ToxB_R1_98_S4_L008_R1_001_x.fastq.gz
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Analysis complete for ToxB_R1_98_S4_L008_R1_001_x.fastq.gz
Started analysis of ToxB_R2_S4_L005_R1_001_x.fastq.gz
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Analysis complete for ToxB_R2_S4_L005_R1_001_x.fastq.gz
Started analysis of ToxA_R1_98_S2_L008_R1_001_x.fastq.gz
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Analysis complete for ToxA_R1_98_S2_L008_R1_001_x.fastq.gz
Started analysis of Control_R1_S14_L008_R1_001_x.fastq.gz
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Analysis complete for Control_R1_S14_L008_R1_001_x.fastq.gz
Started analysis of ToxA_R2_S2_L005_R1_001_x.fastq.gz
Approx 5% complete for ToxA_R2_S2_L005_R1_001_x.fastq.gz
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Analysis complete for ToxA_R2_S2_L005_R1_001_x.fastq.gz
------------------------------------------------
Script completed.
Time elapsed (Quality control) [secs]: 27.890

Sequence quality control completed.




**************************************************
Trimming reads ...
**************************************************
Loading Control_R2_S15_L008_R1_001_x.fastq.gz
Loading ToxB_R1_98_S4_L008_R1_001_x.fastq.gz
Loading ToxB_R2_S4_L005_R1_001_x.fastq.gz
Loading ToxA_R1_98_S2_L008_R1_001_x.fastq.gz
Loading Control_R1_S14_L008_R1_001_x.fastq.gz
Loading ToxA_R2_S2_L005_R1_001_x.fastq.gz
Removing adapters ...
Extracting 20 bp sgRNA sequences ...
Adapter removal completed.
Writing logfiles...
------------------------------------------------
Script completed.
Time elapsed (Read trimming) [secs]: 13.780

Read trimming completed.




**************************************************
Aligning reads ...
**************************************************
Processing sample Control_1 ... 
++++++++++++++++++++++++++++++++++++++++++++++++
Aligning reads to library ...
499804 reads; of these:
  499804 (100.00%) were unpaired; of these:
    26942 (5.39%) aligned 0 times
    408554 (81.74%) aligned exactly 1 time
    64308 (12.87%) aligned >1 times
94.61% overall alignment rate
Alignment completed.
Time elapsed (Alignment) [secs]: 4.952
Analyzing alignment ...
Applying matching threshold ...
Applying ambiguity threshold ...
*** Successfully mapped reads: 337067 (67.4%) ***
Writing alignment logfile ...
Plotting mapping quality ...
Plotting alignment scores ...
Alignment analysis completed.
Time elapsed (Alignment analysis) [secs]: 1.981
Read counting in progress ...
Counting reads per sgRNA ...
Counting reads per gene ...
Read counting completed.
Time elapsed (Read Counting) [secs]: 3.055
Removing raw alignment output...
Time elapsed (Clean-up) [secs]: 0.447
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 10.674

Processing sample Control_2 ... 
++++++++++++++++++++++++++++++++++++++++++++++++
Aligning reads to library ...
499792 reads; of these:
  499792 (100.00%) were unpaired; of these:
    28504 (5.70%) aligned 0 times
    405699 (81.17%) aligned exactly 1 time
    65589 (13.12%) aligned >1 times
94.30% overall alignment rate
Alignment completed.
Time elapsed (Alignment) [secs]: 4.309
Analyzing alignment ...
Applying matching threshold ...
Applying ambiguity threshold ...
*** Successfully mapped reads: 335865 (67.3%) ***
Writing alignment logfile ...
Plotting mapping quality ...
Plotting alignment scores ...
Alignment analysis completed.
Time elapsed (Alignment analysis) [secs]: 2.086
Read counting in progress ...
Counting reads per sgRNA ...
Counting reads per gene ...
Read counting completed.
Time elapsed (Read Counting) [secs]: 2.820
Removing raw alignment output...
Time elapsed (Clean-up) [secs]: 0.037
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 9.499

Processing sample ToxA_1 ... 
++++++++++++++++++++++++++++++++++++++++++++++++
Aligning reads to library ...
499290 reads; of these:
  499290 (100.00%) were unpaired; of these:
    21646 (4.34%) aligned 0 times
    411555 (82.43%) aligned exactly 1 time
    66089 (13.24%) aligned >1 times
95.66% overall alignment rate
Alignment completed.
Time elapsed (Alignment) [secs]: 4.574
Analyzing alignment ...
Applying matching threshold ...
Applying ambiguity threshold ...
*** Successfully mapped reads: 342137 (68.5%) ***
Writing alignment logfile ...
Plotting mapping quality ...
Plotting alignment scores ...
Alignment analysis completed.
Time elapsed (Alignment analysis) [secs]: 1.891
Read counting in progress ...
Counting reads per sgRNA ...
Counting reads per gene ...
Read counting completed.
Time elapsed (Read Counting) [secs]: 2.735
Removing raw alignment output...
Time elapsed (Clean-up) [secs]: 0.038
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 9.474

Processing sample ToxA_2 ... 
++++++++++++++++++++++++++++++++++++++++++++++++
Aligning reads to library ...
499892 reads; of these:
  499892 (100.00%) were unpaired; of these:
    28785 (5.76%) aligned 0 times
    405753 (81.17%) aligned exactly 1 time
    65354 (13.07%) aligned >1 times
94.24% overall alignment rate
Alignment completed.
Time elapsed (Alignment) [secs]: 5.092
Analyzing alignment ...
Applying matching threshold ...
Applying ambiguity threshold ...
*** Successfully mapped reads: 334267 (66.9%) ***
Writing alignment logfile ...
Plotting mapping quality ...
Plotting alignment scores ...
Alignment analysis completed.
Time elapsed (Alignment analysis) [secs]: 1.913
Read counting in progress ...
Counting reads per sgRNA ...
Counting reads per gene ...
Read counting completed.
Time elapsed (Read Counting) [secs]: 2.700
Removing raw alignment output...
Time elapsed (Clean-up) [secs]: 0.024
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 9.963

Processing sample ToxB_1 ... 
++++++++++++++++++++++++++++++++++++++++++++++++
Aligning reads to library ...
499987 reads; of these:
  499987 (100.00%) were unpaired; of these:
    27292 (5.46%) aligned 0 times
    414621 (82.93%) aligned exactly 1 time
    58074 (11.62%) aligned >1 times
94.54% overall alignment rate
Alignment completed.
Time elapsed (Alignment) [secs]: 4.359
Analyzing alignment ...
Applying matching threshold ...
Applying ambiguity threshold ...
*** Successfully mapped reads: 354859 (71.0%) ***
Writing alignment logfile ...
Plotting mapping quality ...
Plotting alignment scores ...
Alignment analysis completed.
Time elapsed (Alignment analysis) [secs]: 1.927
Read counting in progress ...
Counting reads per sgRNA ...
Counting reads per gene ...
Read counting completed.
Time elapsed (Read Counting) [secs]: 2.733
Removing raw alignment output...
Time elapsed (Clean-up) [secs]: 0.039
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 9.324

Processing sample ToxB_2 ... 
++++++++++++++++++++++++++++++++++++++++++++++++
Aligning reads to library ...
499999 reads; of these:
  499999 (100.00%) were unpaired; of these:
    28983 (5.80%) aligned 0 times
    413396 (82.68%) aligned exactly 1 time
    57620 (11.52%) aligned >1 times
94.20% overall alignment rate
Alignment completed.
Time elapsed (Alignment) [secs]: 4.272
Analyzing alignment ...
Applying matching threshold ...
Applying ambiguity threshold ...
*** Successfully mapped reads: 353732 (70.8%) ***
Writing alignment logfile ...
Plotting mapping quality ...
Plotting alignment scores ...
Alignment analysis completed.
Time elapsed (Alignment analysis) [secs]: 1.951
Read counting in progress ...
Counting reads per sgRNA ...
Counting reads per gene ...
Read counting completed.
Time elapsed (Read Counting) [secs]: 2.759
Removing raw alignment output...
Time elapsed (Clean-up) [secs]: 0.021
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 9.239

Read alignments completed.




**************************************************
Averaging read counts ...
**************************************************
Processing Control ...
Averaging read counts over 2 replicates ...
Time elapsed [secs]: 3.733
Processing ToxB ...
Averaging read counts over 2 replicates ...
Time elapsed [secs]: 3.723
Processing ToxA ...
Averaging read counts over 2 replicates ...
Time elapsed [secs]: 3.840
Read count averaging completed.




**************************************************
Normalizing read counts ...
**************************************************
++++++++++++++++++++++++++++++++++++++++++++++++
Normalizing to counts per million reads ...
Processing ToxB_avg ...
Processing Control_avg ...
Processing ToxB_2 ...
Processing ToxA_avg ...
Processing ToxA_1 ...
Processing Control_1 ...
Processing Control_2 ...
Processing ToxA_2 ...
Processing ToxB_1 ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.674

Normalization completed.




**************************************************
Analyzing read counts ...
**************************************************
Processing sample ToxB_avg ... 
++++++++++++++++++++++++++++++++++++++++++++++++
Computing Gini coefficients ... 
Gini Index (sgRNAs): 0.968
Gini Index (genes): 0.895
Plotting Lorenz curves ...
Generating boxplots...
Generating histograms...
Writing distribution file ... 
------------------------------------------------
Script completed.
Time elapsed [secs]: 1.409

Processing sample Control_avg ... 
++++++++++++++++++++++++++++++++++++++++++++++++
Computing Gini coefficients ... 
Gini Index (sgRNAs): 0.664
Gini Index (genes): 0.374
Plotting Lorenz curves ...
Generating boxplots...
Generating histograms...
Writing distribution file ... 
------------------------------------------------
Script completed.
Time elapsed [secs]: 1.439

Processing sample ToxB_2 ... 
++++++++++++++++++++++++++++++++++++++++++++++++
Computing Gini coefficients ... 
Gini Index (sgRNAs): 0.972
Gini Index (genes): 0.904
Plotting Lorenz curves ...
Generating boxplots...
Generating histograms...
Writing distribution file ... 
------------------------------------------------
Script completed.
Time elapsed [secs]: 1.401

Processing sample ToxA_avg ... 
++++++++++++++++++++++++++++++++++++++++++++++++
Computing Gini coefficients ... 
Gini Index (sgRNAs): 0.93
Gini Index (genes): 0.75
Plotting Lorenz curves ...
Generating boxplots...
Generating histograms...
Writing distribution file ... 
------------------------------------------------
Script completed.
Time elapsed [secs]: 1.438

Processing sample ToxA_1 ... 
++++++++++++++++++++++++++++++++++++++++++++++++
Computing Gini coefficients ... 
Gini Index (sgRNAs): 0.95
Gini Index (genes): 0.797
Plotting Lorenz curves ...
Generating boxplots...
Generating histograms...
Writing distribution file ... 
------------------------------------------------
Script completed.
Time elapsed [secs]: 1.440

Processing sample Control_1 ... 
++++++++++++++++++++++++++++++++++++++++++++++++
Computing Gini coefficients ... 
Gini Index (sgRNAs): 0.774
Gini Index (genes): 0.467
Plotting Lorenz curves ...
Generating boxplots...
Generating histograms...
Writing distribution file ... 
------------------------------------------------
Script completed.
Time elapsed [secs]: 1.465

Processing sample Control_2 ... 
++++++++++++++++++++++++++++++++++++++++++++++++
Computing Gini coefficients ... 
Gini Index (sgRNAs): 0.752
Gini Index (genes): 0.445
Plotting Lorenz curves ...
Generating boxplots...
Generating histograms...
Writing distribution file ... 
------------------------------------------------
Script completed.
Time elapsed [secs]: 1.444

Processing sample ToxA_2 ... 
++++++++++++++++++++++++++++++++++++++++++++++++
Computing Gini coefficients ... 
Gini Index (sgRNAs): 0.92
Gini Index (genes): 0.72
Plotting Lorenz curves ...
Generating boxplots...
Generating histograms...
Writing distribution file ... 
------------------------------------------------
Script completed.
Time elapsed [secs]: 1.428

Processing sample ToxB_1 ... 
++++++++++++++++++++++++++++++++++++++++++++++++
Computing Gini coefficients ... 
Gini Index (sgRNAs): 0.971
Gini Index (genes): 0.895
Plotting Lorenz curves ...
Generating boxplots...
Generating histograms...
Writing distribution file ... 
------------------------------------------------
Script completed.
Time elapsed [secs]: 1.409

Read count analysis completed.




**************************************************
Analyzing control distribution ...
**************************************************
++++++++++++++++++++++++++++++++++++++++++++++++
Reading control counts ...
Estimating mean and variance ...
Overdispersion detected at p=0.0. Choosing negative binomial model ...
Computing distribution parameters ...
Writing dataframe ...
Generating dispersion plot ...
Generating log regression plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 3.325

Control analysis completed.




**************************************************
sgRNA enrichment analysis ...
**************************************************
Processing sample ToxB_avg ... 
++++++++++++++++++++++++++++++++++++++++++++++++
Loading read counts ...
Computing fold-changes ...
Computing p-values ...
p-value correction ...
Plotting p-values ...
Writing results dataframe ...
------------------------------------------------
Script completed.
Time elapsed [secs]: 7.001

Processing sample ToxB_2 ... 
++++++++++++++++++++++++++++++++++++++++++++++++
Loading read counts ...
Computing fold-changes ...
Computing p-values ...
p-value correction ...
Plotting p-values ...
Writing results dataframe ...
------------------------------------------------
Script completed.
Time elapsed [secs]: 6.957

Processing sample ToxA_avg ... 
++++++++++++++++++++++++++++++++++++++++++++++++
Loading read counts ...
Computing fold-changes ...
Computing p-values ...
p-value correction ...
Plotting p-values ...
Writing results dataframe ...
------------------------------------------------
Script completed.
Time elapsed [secs]: 7.447

Processing sample ToxA_1 ... 
++++++++++++++++++++++++++++++++++++++++++++++++
Loading read counts ...
Computing fold-changes ...
Computing p-values ...
p-value correction ...
Plotting p-values ...
Writing results dataframe ...
------------------------------------------------
Script completed.
Time elapsed [secs]: 7.093

Processing sample ToxA_2 ... 
++++++++++++++++++++++++++++++++++++++++++++++++
Loading read counts ...
Computing fold-changes ...
Computing p-values ...
p-value correction ...
Plotting p-values ...
Writing results dataframe ...
------------------------------------------------
Script completed.
Time elapsed [secs]: 7.539

Processing sample ToxB_1 ... 
++++++++++++++++++++++++++++++++++++++++++++++++
Loading read counts ...
Computing fold-changes ...
Computing p-values ...
p-value correction ...
Plotting p-values ...
Writing results dataframe ...
------------------------------------------------
Script completed.
Time elapsed [secs]: 6.988

sgRNA enrichment analysis completed.




**************************************************
Read count scatterplots ...
**************************************************
Processing sample ToxB_avg ... 
++++++++++++++++++++++++++++++++++++++++++++++++
Reading counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 1.572

Processing sample ToxB_2 ... 
++++++++++++++++++++++++++++++++++++++++++++++++
Reading counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 1.586

Processing sample ToxA_avg ... 
++++++++++++++++++++++++++++++++++++++++++++++++
Reading counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 1.572

Processing sample ToxA_1 ... 
++++++++++++++++++++++++++++++++++++++++++++++++
Reading counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 1.545

Processing sample ToxA_2 ... 
++++++++++++++++++++++++++++++++++++++++++++++++
Reading counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 1.562

Processing sample ToxB_1 ... 
++++++++++++++++++++++++++++++++++++++++++++++++
Reading counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 1.553

Read count scatterplots completed.




**************************************************
Replicate correlation ...
**************************************************
Processing sample Control ... 
++++++++++++++++++++++++++++++++++++++++++++++++
Sample 1: Control_1 | Sample 2: Control_2
Reading counts ...
Log10 transformation ...
Computing correlation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 1.633

Processing sample ToxB ... 
++++++++++++++++++++++++++++++++++++++++++++++++
Sample 1: ToxB_1 | Sample 2: ToxB_2
Reading counts ...
Log10 transformation ...
Computing correlation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 1.603

Processing sample ToxA ... 
++++++++++++++++++++++++++++++++++++++++++++++++
Sample 1: ToxA_1 | Sample 2: ToxA_2
Reading counts ...
Log10 transformation ...
Computing correlation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 1.608


Replicate correlation analysis completed.




**************************************************
Clustering analysis ...
**************************************************
++++++++++++++++++++++++++++++++++++++++++++++++
Loading read counts ...
Computing variance ...
Extracting top 25 most variable sgRNAs ...
Writing dataframe ...
Plotting heatmap ...
--------------------------------------------
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

--------------------------------------------
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.201

Clustering analysis completed.




**************************************************
Gene ranking analysis ...
**************************************************
Processing sample ToxB_2 ... 
++++++++++++++++++++++++++++++++++++++++++++++++
Loading sgRNA enrichment table ...
Looking for sgRNAs with significant fold change ...
Computing average fold change across sgRNAs ...
Computing aRRA scores ...
Time elapsed (aRRA Computation) [secs]: 3.216
Estimating aRRA null distribution (1000 permutations)...
Time elapsed (aRRA Permutation) [secs]: 0.214
Computing aRRA p-values ...
Plotting p-values ...
Writing results dataframe ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 8.183


Processing sample ToxA_1 ... 
++++++++++++++++++++++++++++++++++++++++++++++++
Loading sgRNA enrichment table ...
Looking for sgRNAs with significant fold change ...
Computing average fold change across sgRNAs ...
Computing aRRA scores ...
Time elapsed (aRRA Computation) [secs]: 3.413
Estimating aRRA null distribution (1000 permutations)...
Time elapsed (aRRA Permutation) [secs]: 0.208
Computing aRRA p-values ...
Plotting p-values ...
Writing results dataframe ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 9.278


Processing sample ToxA_2 ... 
++++++++++++++++++++++++++++++++++++++++++++++++
Loading sgRNA enrichment table ...
Looking for sgRNAs with significant fold change ...
Computing average fold change across sgRNAs ...
Computing aRRA scores ...
Time elapsed (aRRA Computation) [secs]: 4.167
Estimating aRRA null distribution (1000 permutations)...
Time elapsed (aRRA Permutation) [secs]: 0.231
Computing aRRA p-values ...
Plotting p-values ...
Writing results dataframe ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 10.659


Processing sample ToxB_1 ... 
++++++++++++++++++++++++++++++++++++++++++++++++
Loading sgRNA enrichment table ...
Looking for sgRNAs with significant fold change ...
Computing average fold change across sgRNAs ...
Computing aRRA scores ...
Time elapsed (aRRA Computation) [secs]: 3.718
Estimating aRRA null distribution (1000 permutations)...
Time elapsed (aRRA Permutation) [secs]: 0.185
Computing aRRA p-values ...
Plotting p-values ...
Writing results dataframe ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 10.111


Combining gene ranks across replicates ... 
++++++++++++++++++++++++++++++++++++++++++++++++
Reading ToxB replicate 1 ...
Reading ToxB replicate 2 ...
Computing Fisher statistic ...
Writing results dataframe ...
Time elapsed [secs]: 1.066
++++++++++++++++++++++++++++++++++++++++++++++++
Reading ToxA replicate 1 ...
Reading ToxA replicate 2 ...
Computing Fisher statistic ...
Writing results dataframe ...
Time elapsed [secs]: 0.949

Gene ranking analysis completed.




**************************************************
PinAPL-Py completed.
Time elapsed [mins]: 4.118

*** RUN FINISHED SUCCESSFULLY ***
LOADING RESULTS PAGE. PLEASE REFRESH PERIODICALLY...
# Required 
ScreenType: 'enrichment' 
LibFilename: 'GeCKOv21_Human.tsv' 

# Library Parameters 
LibFilename: 'GeCKOv21_Human.tsv'       
seq_5_end: 'TCTTGTGGAAAGGACGAAACACCN'  
NonTargetPrefix: 'NonTargeting'        
NumGuidesPerGene: 6                       
                                       

# Alignment 
sgRNALength: 20 
CutErrorTol: 0.1 
AS_min: 40 
Theta: 2 
L_bw: 11 
N_bw: 1 
i_bw: 'S,1,0.75' 
AlnOutput: 'Delete' 
keepCutReads: False 
delta: 1 
R_min: 20 

# Read Counting 
Normalization: 'cpm' 
Cutoff: 0 
RoundCount: False 
repl_avg: 'median' 

# Gene Ranking 
GeneMetric: 'aRRA' 
Np: 1000 
P_0: 0.01 
thr_STARS: 10 

# Statistical Significance 
alpha_s: 0.01 
alpha_g: 0.01 
padj: 'fdr_bh' 
p_overdisp: 0.01 

# Sample Clustering 
ClusterBy: 'variance' 
TopN: 25 

# Visualization 
dotsize: 10 
TransparencyLevel: 0.1 
scatter_annotate: False 
ShowNonTargets: False 
logbase: 10 
width_p: 800 
height_p: 800 
fontsize_p: 14 
marginsize: 10 
max_q: 95 
svg: True 
dpi: 300 
HitListFormat: 'tsv' 

WorkingDir: '/workingdir/'
DataDir: '/workingdir/Data/'
TempDataDir: '/workingdir/TempData/'
LibDir: '/workingdir/Library/'
IndexDir: '/workingdir/Library/Bowtie2_Index/'
ScriptsDir: '/opt/PinAPL-Py/Scripts/'
AlignDir: '/workingdir/Alignments/'
AnalysisDir: '/workingdir/Analysis/'
TrimLogDir: '/workingdir/Analysis/Read_Trimming'
HitDir: '/workingdir/Analysis/sgRNA_Rankings'
GeneDir: '/workingdir/Analysis/Gene_Rankings'
ControlDir: '/workingdir/Analysis/Control/'
HeatDir: '/workingdir/Analysis/Heatmap/'
AlnQCDir: '/workingdir/Analysis/Alignment_Statistics/'
CountQCDir: '/workingdir/Analysis/ReadCount_Statistics/'
ScatterDir: '/workingdir/Analysis/ReadCount_Scatterplots/'
HiLiteDir: '/workingdir/Analysis/ReadCount_Scatterplots/Highlighted_Genes/'
CorrelDir: '/workingdir/Analysis/Replicate_Correlation/'
HiLiteDir2: '/workingdir/Analysis/Replicate_Correlation/Highlighted_Genes'
EffDir: '/workingdir/Analysis/sgRNA_Efficacy/'
DepthDir: '/workingdir/Analysis/Read_Depth/'
SeqQCDir: '/workingdir/Analysis/Sequence_Quality/'
pvalDir: '/workingdir/Analysis/p-values/' 
LogFileDir: '/workingdir/Analysis/Log_File/'
bw2Dir: '/usr/bin/'
CutAdaptDir: '/root/.local/bin/'   
STARSDir: '/opt/PinAPL-Py/Scripts/STARS_mod/'

SanityScript: 'CheckCharacters'
IndexScript: 'BuildLibraryIndex'
LoaderScript: 'LoadDataSheet'
ReadDepthScript: 'PlotNumReads'
SeqQCScript: 'CheckSequenceQuality'
TrimScript: 'TrimReads'
AlignScript: 'AlignReads'
NormalizeScript: 'NormalizeReadCounts'
AverageCountsScript: 'AverageCounts'
StatsScript: 'AnalyzeReadCounts'
ControlScript: 'AnalyzeControl'
sgRNARankScript: 'FindHits'
GeneRankScript: 'RankGenes'
CombineScript: 'CombineGeneRanks'
ScatterScript: 'PlotCounts'
ReplicateScript: 'PlotReplicates'
ClusterScript: 'PlotHeatmap'
Filename Sample Name
Control_R1_S14_L008_R1_001_x.fastq.gz Control_1
Control_R2_S15_L008_R1_001_x.fastq.gz Control_2
ToxA_R1_98_S2_L008_R1_001_x.fastq.gz ToxA_1
ToxA_R2_S2_L005_R1_001_x.fastq.gz ToxA_2
ToxB_R1_98_S4_L008_R1_001_x.fastq.gz ToxB_1
ToxB_R2_S4_L005_R1_001_x.fastq.gz ToxB_2