Merge pull request #51 from torres-alexis/dppd-multiqc-update

Document updates 
- typo fixes
- plot size corrections
- specifying the zip command for multiqc reports to match what's published on the OSDR

Author: asaravia-butler

Microarray/Affymetrix/Pipeline_GL-DPPD-7114_Versions/GL-DPPD-7114.md

@@ -65,7 +65,7 @@ Lauren Sanders (acting GeneLab Project Scientist)
 |biomaRt|2.50.0|[https://bioconductor.org/packages/3.14/bioc/html/biomaRt.html](https://bioconductor.org/packages/3.14/bioc/html/biomaRt.html)|
 |matrixStats|0.63.0|[https://github.com/HenrikBengtsson/matrixStats](https://github.com/HenrikBengtsson/matrixStats)|
 |statmod|1.5.0|[https://github.com/cran/statmod](https://github.com/cran/statmod)|
-|dp_tools|1.3.2|[https://github.com/J-81/dp_tools](https://github.com/J-81/dp_tools)|
+|dp_tools|1.3.4|[https://github.com/J-81/dp_tools](https://github.com/J-81/dp_tools)|
 |singularity|3.9|[https://sylabs.io](https://sylabs.io)|
 |Quarto|1.1.251|[https://quarto.org](https://quarto.org)|
 
@@ -292,7 +292,7 @@ legend("topright", legend = colnames(raw_data@assayData$exprs),
         lty = c(1,2,3,4,5), # Seems like oligo::hist cycles through these first five line types
         col = oligo::darkColors(n = ncol(raw_data)), # Ensure legend color is in sync with plot
         ncol = number_of_sets, # Set number of columns by number of sets
-        cex = 1 + 0.2 - (number_of_sets*0.2) # Reduce scale by 20% for each column beyond 1
+        cex = max(0.35, 1 + 0.2 - (number_of_sets*0.2)) # Reduce scale by 20% for each column beyond 1 with minimum of 35%
       )
 
 # Reset par
@@ -475,7 +475,7 @@ legend("topright", legend = colnames(norm_data@assayData$exprs),
         lty = c(1,2,3,4,5), # Seems like oligo::hist cycles through these first five line types
         col = oligo::darkColors(n = ncol(norm_data)), # Ensure legend color is in sync with plot
         ncol = number_of_sets, # Set number of columns by number of sets
-        cex = 1 + 0.2 - (number_of_sets*0.2) # Reduce scale by 20% for each column beyond 1
+        cex = max(0.35, 1 + 0.2 - (number_of_sets*0.2)) # Reduce scale by 20% for each column beyond 1 with minimum of 35%
       )
 
 # Reset par
@@ -1219,4 +1219,4 @@ write.csv(norm_data_matrix_annotated, file.path(DIR_NORMALIZED_EXPRESSION, "norm
 - **raw_intensities_probe.csv** (table containing the background corrected, unnormalized probe intensity values for each sample including gene annotations. The ProbeID is the unique index column.)
 - **normalized_intensities_probe.csv** (table containing the background corrected, normalized probe intensity values for each sample including gene annotations.  The ProbeID is the unique index column.)
 
-> All steps of the Microarray pipeline are performed using R markdown and the completed R markdown is rendered (via Quarto) as an html file (**NF_MAAffymetrix_\*.html**) and published in the [Open Science Data Repository (OSDR)](https://osdr.nasa.gov/bio/repo/) for the respective dataset.
+> All steps of the Microarray pipeline are performed using R markdown and the completed R markdown is rendered (via Quarto) as an html file (**NF_MAAffymetrix_\*.html**) and published in the [Open Science Data Repository (OSDR)](https://osdr.nasa.gov/bio/repo/) for the respective dataset.

RNAseq/Pipeline_GL-DPPD-7101_Versions/GL-DPPD-7101-F.md

@@ -168,7 +168,8 @@ fastqc -o /path/to/raw_fastqc/output/directory *.fastq.gz
 ### 1b. Compile Raw Data QC  
 
 ```bash
-multiqc --interactive -n raw_multiqc -o /path/to/raw_multiqc/output/directory /path/to/directory/containing/raw_fastqc/files
+multiqc --interactive -n raw_multiqc -o /path/to/raw_multiqc/output/raw_multiqc_report /path/to/directory/containing/raw_fastqc/files
+zip -r raw_multiqc_report.zip /path/to/raw_multiqc/output/raw_multiqc_report
 ```
 
 **Parameter Definitions:**
@@ -184,8 +185,9 @@ multiqc --interactive -n raw_multiqc -o /path/to/raw_multiqc/output/directory /p
 
 **Output Data:**
 
-- **raw_multiqc.html** (multiqc report)
-- **/raw_multiqc_data** (directory containing multiqc data)
+* **raw_multiqc_report.zip** (zip containing the following)
+  * **raw_multiqc.html** (multiqc output html summary)
+  * **raw_multiqc_data** (directory containing multiqc output data)
 
 <br>
 
@@ -257,7 +259,8 @@ fastqc -o /path/to/trimmed_fastqc/output/directory *.fastq.gz
 ### 2c. Compile Trimmed Data QC  
 
 ```bash
-multiqc --interactive -n trimmed_multiqc -o /path/to/trimmed_multiqc/output/directory /path/to/directory/containing/trimmed_fastqc/files
+multiqc --interactive -n trimmed_multiqc -o /path/to/trimmed_multiqc/output/trimmed_multiqc_report /path/to/directory/containing/trimmed_fastqc/files
+zip -r trimmed_multiqc_report.zip /path/to/trimmed_multiqc/output/trimmed_multiqc_report
 ```
 
 **Parameter Definitions:**
@@ -273,8 +276,9 @@ multiqc --interactive -n trimmed_multiqc -o /path/to/trimmed_multiqc/output/dire
 
 **Output Data:**
 
-- **trimmed_multiqc.html** (multiqc report)
-- **/trimmed_multiqc_data** (directory containing multiqc data)
+* **trimmed_multiqc_report.zip** (zip containing the following)
+  * **trimmed_multiqc.html** (multiqc output html summary)
+  * **trimmed_multiqc_data** (directory containing multiqc output data)
 
 <br>
 
@@ -420,7 +424,8 @@ STAR --twopassMode Basic \
 ### 4b. Compile Alignment Logs
 
 ```bash
-multiqc --interactive -n align_multiqc -o /path/to/aligned_multiqc/output/directory /path/to/*Log.final.out/files
+multiqc --interactive -n align_multiqc -o /path/to/align_multiqc/output/align_multiqc_report /path/to/*Log.final.out/files
+zip -r align_multiqc_report.zip /path/to/align_multiqc/output/align_multiqc_report
 ```
 
 **Parameter Definitions:**
@@ -436,8 +441,9 @@ multiqc --interactive -n align_multiqc -o /path/to/aligned_multiqc/output/direct
 
 **Output Data:**
 
-- **align_multiqc.html** (multiqc report)
-- **/align_multiqc_data** (directory containing multiqc data)
+* **align_multiqc_report.zip** (zip containing the following)
+  * **align_multiqc.html** (multiqc output html summary)
+  * **align_multiqc_data** (directory containing multiqc output data)
 
 <br>
 
@@ -628,7 +634,8 @@ infer_experiment.py -r /path/to/annotation/BED/file \
 ### 6b. Compile Strandedness Reports
 
 ```bash
-multiqc --interactive -n infer_exp_multiqc -o /path/to/infer_exp_multiqc/output/directory /path/to/*infer_expt.out/files
+multiqc --interactive -n infer_exp_multiqc -o /path/to/infer_exp_multiqc/output/infer_exp_multiqc /path/to/*infer_expt.out/files
+zip -r infer_exp_multiqc_report.zip /path/to/infer_exp_multiqc/output/infer_exp_multiqc_report
 ```
 
 **Parameter Definitions:**
@@ -644,8 +651,9 @@ multiqc --interactive -n infer_exp_multiqc -o /path/to/infer_exp_multiqc/output/
 
 **Output Data:**
 
-- **infer_exp_multiqc.html** (multiqc report)
-- **/infer_exp_multiqc_data** (directory containing multiqc data)
+* **infer_exp_multiqc_report.zip** (zip containing the following)
+  * **infer_exp_multiqc.html** (multiqc output html summary)
+  * **infer_exp_multiqc_data** (directory containing multiqc output data)
 
 <br>
 
@@ -681,7 +689,8 @@ geneBody_coverage.py -r /path/to/annotation/BED/file \
 ### 6d. Compile GeneBody Coverage Reports
 
 ```bash
-multiqc --interactive -n genebody_cov_multiqc -o /path/to/geneBody_coverage_multiqc/output/directory /path/to/geneBody_coverage/output/files
+multiqc --interactive -n genebody_cov_multiqc -o /path/to/geneBody_cov_multiqc/output/geneBody_cov_multiqc_report /path/to/geneBody_coverage/output/files
+zip -r genebody_cov_multiqc_report.zip /path/to/genebody_cov_multiqc/output/genebody_cov_multiqc_report
 ```
 
 **Parameter Definitions:**
@@ -697,8 +706,9 @@ multiqc --interactive -n genebody_cov_multiqc -o /path/to/geneBody_coverage_mult
 
 **Output Data:**
 
-- **geneBody_cov_multiqc.html** (multiqc report)
-- **/geneBody_cov_multiqc_data** (directory containing multiqc data)
+* **genebody_cov_multiqc_report.zip** (zip containing the following)
+  * **genebody_cov_multiqc.html** (multiqc output html summary)
+  * **genebody_cov_multiqc_data** (directory containing multiqc output data)
 
 <br>
 
@@ -740,7 +750,8 @@ inner_distance.py -r /path/to/annotation/BED/file \
 ### 6f. Compile Inner Distance Reports
 
 ```bash
-multiqc --interactive -n inner_dist_multiqc /path/to/inner_dist_multiqc/output/directory /path/to/inner_dist/output/files
+multiqc --interactive -n inner_dist_multiqc /path/to/align_multiqc/output/inner_dist_multiqc_report /path/to/inner_dist/output/files
+zip -r inner_dist_multiqc_report.zip /path/to/align_multiqc/output/inner_dist_multiqc_report
 ```
 
 **Parameter Definitions:**
@@ -756,8 +767,9 @@ multiqc --interactive -n inner_dist_multiqc /path/to/inner_dist_multiqc/output/d
 
 **Output Data:**
 
-- **inner_distance_multiqc.html** (multiqc report)
-- **/inner_distance_multiqc_data** (directory containing multiqc data)
+* **inner_dist_multiqc_report.zip** (zip containing the following)
+  * **inner_dist_multiqc.html** (multiqc output html summary)
+  * **inner_dist_multiqc_data** (directory containing multiqc output data)
 
 <br>
 
@@ -790,7 +802,8 @@ read_distribution.py -r /path/to/annotation/BED/file \
 ### 6h. Compile Read Distribution Reports
 
 ```bash
-multiqc --interactive -n read_dist_multiqc -o /path/to/read_dist_multiqc/output/directory /path/to/*read_dist.out/files
+multiqc --interactive -n read_dist_multiqc -o /path/to/read_dist_multiqc/output/read_dist_multiqc_report /path/to/*read_dist.out/files
+zip -r read_dist_multiqc_report.zip /path/to/read_dist_multiqc/output/read_dist_multiqc_report
 ```
 
 **Parameter Definitions:**
@@ -806,8 +819,9 @@ multiqc --interactive -n read_dist_multiqc -o /path/to/read_dist_multiqc/output/
 
 **Output Data:**
 
-- **read_dist_multiqc.html** (multiqc report)
-- **/read_dist_multiqc_data** (directory containing multiqc data)
+* **read_dist_multiqc_report.zip** (zip containing the following)
+  * **read_dist_multiqc.html** (multiqc output html summary)
+  * **read_dist_multiqc_data** (directory containing multiqc output data)
 
 <br>
 
@@ -819,7 +833,6 @@ multiqc --interactive -n read_dist_multiqc -o /path/to/read_dist_multiqc/output/
 rsem-prepare-reference --gtf /path/to/annotation/gtf/file \
  /path/to/genome/fasta/file \
  /path/to/RSEM/genome/directory/RSEM_ref_prefix
-
 ```
 
 **Parameter Definitions:**
@@ -904,7 +917,8 @@ rsem-calculate-expression --num-threads NumberOfThreads \
 ### 8b. Compile RSEM Count Logs
 
 ```bash
-multiqc --interactive -n RSEM_count_multiqc -o /path/to/RSEM_count_multiqc/output/directory /path/to/*stat/files
+multiqc --interactive -n RSEM_count_multiqc -o /path/to/RSEM_count_multiqc/output/RSEM_count_multiqc_report /path/to/*stat/files
+zip -r RSEM_count_multiqc_report.zip /path/to/raw_multiqc/output/RSEM_count_multiqc_report
 ```
 
 **Parameter Definitions:**
@@ -923,8 +937,9 @@ multiqc --interactive -n RSEM_count_multiqc -o /path/to/RSEM_count_multiqc/outpu
 
 **Output Data:**
 
-- **RSEM_count_multiqc.html** (multiqc report)
-- **/RSEM_count_multiqc_data** (directory containing multiqc data)
+* **RSEM_count_multiqc_report.zip** (zip containing the following)
+  * **RSEM_count_multiqc.html** (multiqc output html summary)
+  * **RSEM_count_multiqc_data** (directory containing multiqc output data)
 
 <br>
 

Raw_Data_Generation/UPX_kit_for_bulk_RNAseq/Pipeline_GL-DPPD-7108_Versions/GL-DPPD-7108.md

@@ -2,7 +2,7 @@
 
 > **This page holds an overview and instructions for how GeneLab generates raw (bulk) RNA sequence data from libraries prepared [in-house](https://genelab.nasa.gov/genelab-sequencing-services/omics_data) using the [Qiagen UPX kit](https://www.qiagen.com/us/products/discovery-and-translational-research/next-generation-sequencing/rna-sequencing/three-rnaseq/qiaseq-upx-3-transcriptome-kits/). Raw data output files and processing protocol are provided for each GeneLab-generated GLDS dataset hosted in the [Open Science Data Repository (OSDR)](https://osdr.nasa.gov/bio/repo/).
 > The instructions below assume that the samples were prepared as follows:**
-> 1. Bulk RNA was was extracted from samples 
+> 1. Bulk RNA was extracted from samples 
 > 2. Each sample was prepared with a unique cell ID
 > 3. Samples were pooled together to create sample pools
 > 4. Each sample pool was prepared with a unique single index