update docs for hs1, quality and controls

CCBR · Feb 10, 2023 · ddbbf6d · ddbbf6d
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diff --git a/docs/user-guide/contributions.md b/docs/user-guide/contributions.md
@@ -1,9 +1,10 @@
 # Contributions
-The following members contributed to the development of the iCLIP pipeline:
+The following members contributed to the development of the CARLISLE pipeline:
 
 - [Vishal Koparde](https://github.com/kopardev)
 - [Samantha Sevilla](https://github.com/slsevilla)
 - Sohyoung Kim
 - Vassiliki Saloura
+- [Hsien-chao Chou](https://github.com/hsienchao)
 
-VK, SS, SK contributed to the generating the source code and all members contributed to the main concepts and analysis.
+VK, SS, SK, HC contributed to the generating the source code and all members contributed to the main concepts and analysis.
diff --git a/docs/user-guide/getting-started.md b/docs/user-guide/getting-started.md
@@ -4,7 +4,7 @@ The CARLISLE github repository is stored locally, and will be used for project d
 ## 1. Getting Started
 
 ## 1.1 Introduction
-The CARLISLE Pipelie beings with raw FASTQ files and performs trimming followed by alignment using [BOWTIE2](https://bowtie-bio.sourceforge.net/bowtie2/index.shtml). Data is then normalized through either the use of an user-species species (IE E.Coli) spike-in control or through the determined library size. Peaks are then called using [MACS2](https://hbctraining.github.io/Intro-to-ChIPseq/lessons/05_peak_calling_macs.html), [SEACR](https://github.com/FredHutch/SEACR), and [GoPEAKS](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02707-w) with various options selected by the user. Peaks are then annotated, and summarized into reports. If designated, differential analysis is performed using [DESEQ2](https://bioconductor.org/packages/release/bioc/html/DESeq2.html). QC reports are also generated with each project.
+The CARLISLE Pipelie beings with raw FASTQ files and performs trimming followed by alignment using [BOWTIE2](https://bowtie-bio.sourceforge.net/bowtie2/index.shtml). Data is then normalized through either the use of an user-species species (IE E.Coli) spike-in control or through the determined library size. Peaks are then called using [MACS2](https://hbctraining.github.io/Intro-to-ChIPseq/lessons/05_peak_calling_macs.html), [SEACR](https://github.com/FredHutch/SEACR), and [GoPEAKS](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02707-w) with various options selected by the user. Peaks are then annotated, and summarized into reports. If designated, differential analysis is performed using [DESEQ2](https://bioconductor.org/packages/release/bioc/html/DESeq2.html). QC reports are also generated with each project using [FASTQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and [MULTIQC](https://multiqc.info/). Annotations are added using [HOMER](http://homer.ucsd.edu/homer/ngs/annotation.html) and [ROSE](https://github.com/stjude/ROSE).
 
 The following are sub-commands used within CARLISLE:
 
@@ -16,6 +16,7 @@ The following are sub-commands used within CARLISLE:
 - unlock: unlock directory
 - DAG: create DAG report
 - report: create SNAKEMAKE report
+- testrun: copies test manifests and files to WORKDIR
 
 ## 1.2 Setup Dependencies
 CARLISLE has several dependencies listed below. These dependencies can be installed by a sysadmin. All dependencies will be automatically loaded if running from Biowulf.
@@ -36,6 +37,27 @@ CARLISLE has several dependencies listed below. These dependencies can be instal
 - seacr: "seacr/1.4-beta.2"
 - ucsc: "ucsc/407"
 
+bedtools: "bedtools/2.30.0"
+bedops: "bedops/2.4.40"
+bowtie2: "bowtie/2-2.4.2"
+cutadapt: "cutadapt/1.18"
+fastqc: "fastqc/0.11.9"
+fastq_screen: "fastq_screen/0.15.2"
+fastq_val: "fastq_val/0.1.1"
+fastxtoolkit: "fastxtoolkit/0.0.14"
+gopeaks: "github clone https://github.com/maxsonBraunLab/gopeaks"
+homer: "homer/4.11.1"
+macs2: "macs/2.2.7.1"
+multiqc: "multiqc/1.9"
+perl: "perl/5.34.0"
+picard: "picard/2.26.9"
+python37: "python/3.7"
+R: "R/4.2.2"
+rose: "ROSE/1.3.1"
+samtools: "samtools/1.15"
+seacr: "seacr/1.4-beta.2"
+ucsc: "ucsc/407"
+
 ## 1.3 Login to the cluster
 CARLISLE has been exclusively tested on Biowulf HPC. Login to the cluster's head node and move into the pipeline location.
 ```

diff --git a/docs/user-guide/preparing-files.md b/docs/user-guide/preparing-files.md
@@ -80,13 +80,30 @@ peaktype: "norm.stringent.bed, norm.relaxed.bed"
 peaktype: "narrowGo_peaks.bed, broadGo_peaks.bed"
 ```
 A complete list of the available peak calling parameters and the recommended list of parameters is provided below:
-```
-# Complete list
-peaktype: "narrowPeak, broadPeak, norm.stringent.bed, norm.relaxed.bed, non.stringent.bed, non.relaxed.bed, narrowGo_peaks.bed, broadGo_peaks.bed"
 
+| Peak Caller | Narrow | Broad | Normalized, Stringent | Normalized, Relaxed | Non-Normalized, Stringent | Non-Normalized, Relaxed |
+| --- | --- | --- | --- | --- | --- | --- |
+| Macs2 | narrowPeak | broadPeak | NA | NA | NA | NA |
+| SEACR | NA | NA | norm.stringent.bed | norm.relaxed.bed | non.stringent.bed | non.relaxed.bed |
+| GoPeaks | narrowGo_peaks.bed | broadGo_peaks.bed | NA | NA | NA | NA |
+
+```
 # Recommended list
 # peaktype: "narrowPeak, broadPeak, norm.stringent.bed, norm.relaxed.bed, narrowGo_peaks.bed, broadGo_peaks.bed"
 ```
+##### 2.1.3.1.3.1 Macs2 additional option
+MACS2 can be run with or without the control. adding a control will increase peak specificity
+Selecting "Y" for the `macs2_control` will run the paired control sample provided in the sample manifest
+
+##### 2.1.3.1.4 Quality Tresholds
+Thresholds for quality can be controled through the `quality_tresholds` parameter. This must be a list of comma separated values. minimum of numeric value required.
+- default MACS2 qvalue is 0.05 https://manpages.ubuntu.com/manpages/xenial/man1/macs2_callpeak.1.html
+- default GOPEAKS pvalue is 0.05 https://github.com/maxsonBraunLab/gopeaks/blob/main/README.md
+- default SEACR FDR threshold 1 https://github.com/FredHutch/SEACR/blob/master/README.md
+```
+#default values
+quality_thresholds: "0.1, 0.05, 0.01"
+```
 
 #### 2.1.3.2 References
 Additional reference files may be added to the pipeline, if other species were to be used. 

diff --git a/docs/user-guide/test-info.md b/docs/user-guide/test-info.md
@@ -22,29 +22,39 @@ bash ./path/to/dir/carlisle --runmode=testrun --workdir=/path/to/output/dir
 
 - An expected output for the `testrun` is as follows:
 ```
+Job stats:
 job                              count    min threads    max threads
 -----------------------------  -------  -------------  -------------
-DESeq                                6              1              1
-DESeq2                               6              1              1
-align                                6             56             56
-alignstats                           6              2              2
+DESeq                               60              1              1
+DESeq2                              60              1              1
+align                                9             56             56
+alignstats                           9              2              2
 all                                  1              1              1
-bam2bg                              12              2              2
-bed2bb                               5              2              2
-contrast_init                        1              1              1
+bam2bg                              18              4              4
+bed2bb_gopeaks                      48              2              2
+bed2bb_seacr                        48              2              2
+contrast_init                        3              1              1
 create_reference                     1             32             32
 create_replicate_sample_table        1              1              1
-diffbb                               6              1              1
-filter                              12              2              2
+diffbb                              60              1              1
+filter                              18              2              2
+findMotif                          240              6              6
 gather_alignstats                    1              1              1
-macs2                               12              2              2
-make_counts_matrix                   6              1              1
-make_inputs                          6              1              1
-peak2bb                             12              2              2
-seacr                                5              2              2
-trim                                 6             56             56
-venn                                 6              1              1
-total                              117              1             56
+gopeaks                             48              8              8
+macs2                               54              2              2
+make_counts_matrix                  60              1              1
+make_inputs                         60              1              1
+multiqc                              1              1              1
+peak2bb_macs2                       54              2              2
+peakAnnotation_macs2                54              1              1
+peakAnnotation_s_and_g             192              1              1
+qc_fastq_screen_validator            9              4              4
+qc_fastqc                            9              1              1
+rose                               240              2              2
+seacr                               48              2              2
+trim                                 9             56             56
+venn                                60              1              1
+total                             1475              1             56
 ```
 
 ## 5.3 Review outputs