Explore Workflows

https://github.com/ncbi/pgap.git

Path: task_types/tt_align_sort_sa.cwl

Branch/Commit ID: 6d8d29a2156b93a75f1d1c6952738bd63f6bd98e

Workflow to run GetBaseCountsMultiSample fillout on a number of samples, each with their own bam and maf files

https://github.com/mskcc/pluto-cwl.git

Path: cwl/igv-report_maf_workflow.cwl

Branch/Commit ID: 462f6015c9268a4205b6e81de018a470b8a4a153

Cell Ranger Build V(D)J Reference Indices Build a Cell Ranger V(D)J-compatible reference folder from a user-supplied genome FASTA and gene GTF files.

https://github.com/datirium/workflows.git

Path: workflows/cellranger-mkvdjref.cwl

Branch/Commit ID: 22880e0f41d0420a17d643e8a6e8ee18165bbfbf

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/downsampled_alignment.cwl

Branch/Commit ID: c6bbd4cdd612b3b5cc6e9000df4800c21e192bf5

https://github.com/common-workflow-language/cwltool.git

Path: cwltool/schemas/v1.0/v1.0/step-valuefrom-wf.cwl

Branch/Commit ID: 3ed10d0ea7ac57550433a89a92bdbe756bdb0e40

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **pair-end** experiment. A corresponded input [FASTQ](http://maq.sourceforge.net/fastq.shtml) file has to be provided. Current workflow should be used only with the single-end RNA-Seq data. It performs the following steps: 1. Trim adapters from input FASTQ files 2. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 4. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 5. Generate BigWig file on the base of sorted BAM file 6. Map input FASTQ files to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 7. Calculate isoform expression level for the sorted BAM file and GTF/TAB annotation file using GEEP reads-counting utility; export results to file

https://github.com/datirium/workflows.git

Path: workflows/trim-rnaseq-pe.cwl

Branch/Commit ID: 36fd18f11e939d3908b1eca8d2939402f7a99b0f

Inspect provided directory and return filenames. Generate a new directory and return it (including content).

https://github.com/common-workflow-language/cwltool.git

Path: tests/wf/directory.cwl

Branch/Commit ID: bbe20f54deea92d9c9cd38cb1f23c4423133d3de

# Differential gene expression analysis This differential gene expression (DGE) analysis takes as input samples from two experimental conditions that have been processed with an RNA-Seq workflow (see list of \"Upstream workflows\" below). DESeq estimates variance-mean dependence in count data from high-throughput sequencing assays, then tests for DGE based on a model which assumes a negative binomial distribution of gene expression (aligned read count per gene). ### Experimental Setup and Results Interpretation The workflow design uses as its fold change (FC) calculation: condition 1 (c1, e.g. treatment) over condition 2 (c2, e.g. control). In other words: `FC == (c1/c2)` Therefore: - if FC<1 the log2(FC) is <0 (negative), meaning expression in condition1<condition2 (gene is downregulated in c1) - if FC>1 the log2(FC) is >0 (positive), meaning expression in condition1>condition2 (gene is upregulated in c1) In other words, if you have input TREATMENT samples as condition 1, and CONTROL samples as condition 2, a positive L2FC for a gene indicates that expression of the gene in TREATMENT is greater (or upregulated) compared to CONTROL. Next, threshold the p-adjusted values with your FDR (false discovery rate) cutoff to determine if the change may be considered significant or not. It is important to note when DESeq1 or DESeq2 is used in our DGE analysis workflow. If a user inputs only a single sample per condition DESeq1 is used for calculating DGE. In this experimental setup, there are no repeated measurements per gene per condition, therefore biological variability in each condition cannot be captured so the output p-values are assumed to be purely \"technical\". On the other hand, if >1 sample(s) are input per condition DESeq2 is used. In this case, biological variability per gene within each condition is available to be incorporated into the model, and resulting p-values are assumed to be \"biological\". Additionally, DESeq2 fold change is \"shrunk\" to account for sample variability, and as Michael Love (DESeq maintainer) puts it, \"it looks at the largest fold changes that are not due to low counts and uses these to inform a prior distribution. So the large fold changes from genes with lots of statistical information are not shrunk, while the imprecise fold changes are shrunk. This allows you to compare all estimated LFC across experiments, for example, which is not really feasible without the use of a prior\". In either case, the null hypothesis (H0) tested is that there are no significantly differentially expressed genes between conditions, therefore a smaller p-value indicates a lower probability of the H0 occurring by random chance and therefore, below a certain threshold (traditionally <0.05), H0 should be rejected. Additionally, due to the many thousands of independent hypotheses being tested (each gene representing an independent test), the p-values attained by the Wald test are adjusted using the Benjamini and Hochberg method by default. These \"padj\" values should be used for determination of significance (a reasonable value here would be <0.10, i.e. below a 10% FDR). Further Analysis: Output from the DESeq workflow may be used as input to the GSEA (Gene Set Enrichment Analysis) workflow for identifying enriched marker gene sets between conditions. ### DESeq1 High-throughput sequencing assays such as RNA-Seq, ChIP-Seq or barcode counting provide quantitative readouts in the form of count data. To infer differential signal in such data correctly and with good statistical power, estimation of data variability throughout the dynamic range and a suitable error model are required. Simon Anders and Wolfgang Huber propose a method based on the negative binomial distribution, with variance and mean linked by local regression and present an implementation, [DESeq](http://www.bioconductor.org/packages/3.8/bioc/html/DESeq.html), as an R/Bioconductor package. ### DESeq2 In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. [DESeq2](http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html), a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. ### __References__ - Anders S, Huber W (2010). “Differential expression analysis for sequence count data.” Genome Biology, 11, R106. doi: 10.1186/gb-2010-11-10-r106, http://genomebiology.com/2010/11/10/R106/. - Love MI, Huber W, Anders S (2014). “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” Genome Biology, 15, 550. doi: 10.1186/s13059-014-0550-8.

https://github.com/datirium/workflows.git

Path: workflows/deseq.cwl

Branch/Commit ID: 36fd18f11e939d3908b1eca8d2939402f7a99b0f

Genomic regions intersection and visualization ============================================== 1. Merges intervals within each of the filtered peaks files from ChIP/ATAC experiments 2. Overlaps merged intervals and assigns the nearest genes to them

https://github.com/datirium/workflows.git

Path: workflows/intervene.cwl

Branch/Commit ID: c0ca7b140d776eec223ceb1c620eda17281860c4

https://github.com/genome/analysis-workflows.git

Path: definitions/pipelines/tumor_only_detect_variants.cwl

Branch/Commit ID: 44ada20f3eeb59005d5bd999d2435102e9bae991