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Runs DESeq2 using LRT (Likelihood Ratio Test) ============================================= The LRT examines two models for the counts, a full model with a certain number of terms and a reduced model, in which some of the terms of the full model are removed. The test determines if the increased likelihood of the data using the extra terms in the full model is more than expected if those extra terms are truly zero. The LRT is therefore useful for testing multiple terms at once, for example testing 3 or more levels of a factor at once, or all interactions between two variables. The LRT for count data is conceptually similar to an analysis of variance (ANOVA) calculation in linear regression, except that in the case of the Negative Binomial GLM, we use an analysis of deviance (ANODEV), where the deviance captures the difference in likelihood between a full and a reduced model. When one performs a likelihood ratio test, the p values and the test statistic (the stat column) are values for the test that removes all of the variables which are present in the full design and not in the reduced design. This tests the null hypothesis that all the coefficients from these variables and levels of these factors are equal to zero. The likelihood ratio test p values therefore represent a test of all the variables and all the levels of factors which are among these variables. However, the results table only has space for one column of log fold change, so a single variable and a single comparison is shown (among the potentially multiple log fold changes which were tested in the likelihood ratio test). This indicates that the p value is for the likelihood ratio test of all the variables and all the levels, while the log fold change is a single comparison from among those variables and levels. **Technical notes** 1. At least two biological replicates are required for every compared category 2. Metadata file describes relations between compared experiments, for example ``` ,time,condition DH1,day5,WT DH2,day5,KO DH3,day7,WT DH4,day7,KO DH5,day7,KO ``` where `time, condition, day5, day7, WT, KO` should be a single words (without spaces) and `DH1, DH2, DH3, DH4, DH5` correspond to the experiment aliases set in **RNA-Seq experiments** input. 3. Design and reduced formulas should start with **~** and include categories or, optionally, their interactions from the metadata file header. See details in DESeq2 manual [here](https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#interactions) and [here](https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#likelihood-ratio-test) 4. Contrast should be set based on your metadata file header and available categories in a form of `Factor Numerator Denominator`, where `Factor` - column name from metadata file, `Numerator` - category from metadata file to be used as numerator in fold change calculation, `Denominator` - category from metadata file to be used as denominator in fold change calculation. For example `condition WT KO`.

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

Path: workflows/deseq-lrt.cwl

Branch/Commit ID: 480e99a4bb3046e0565113d9dca294e0895d3b0c

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

Path: cwltool/schemas/v1.0/v1.0/step-valuefrom2-wf.cwl

Branch/Commit ID: 4700fbee9a5a3271eef8bc9ee595619d0720431b

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

Path: definitions/subworkflows/vcf_eval_cle_gold.cwl

Branch/Commit ID: a59a803e1809a8fbfabca6b8962a8ad66dd01f1d

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/scatter-wf4.cwl

Branch/Commit ID: 0e37d46e793e72b7c16b5ec03e22cb3ce1f55ba3

Packed ID: main

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

Path: task_types/tt_align_merge_sas.cwl

Branch/Commit ID: 4533a5e930305c674057bc4cf5dda4f39d39b5df

https://github.com/proteinswebteam/ebi-metagenomics-cwl.git

Path: tools/SSU-from-tablehits.cwl

Branch/Commit ID: 9c57dba558a4e04a1884eae1df8431dcaccafc1e

https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git

Path: workflows/emg-pipeline-v3.cwl

Branch/Commit ID: 0cd2d70d63a8ceb2de28f0faac19c919a7bd35ff

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **paired-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 paired-end RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 3. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 4. Generate BigWig file on the base of sorted BAM file 5. Map input FASTQ files to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 6. 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/rnaseq-pe.cwl

Branch/Commit ID: 9e3c3e65c19873cd1ed3cf7cc3b94ebc75ae0cc5

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

Path: definitions/subworkflows/bam_to_bqsr.cwl

Branch/Commit ID: 39ac49f5d080bbb6bfa97246f46a5b621254f622

### Pipeline for Lexogen's QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina [Lexogen original documentation](https://www.lexogen.com/quantseq-3mrna-sequencing/) * Cost-saving and streamlined globin mRNA depletion during QuantSeq library preparation * Genome-wide analysis of gene expression * Cost-efficient alternative to microarrays and standard RNA-Seq * Down to 100 pg total RNA input * Applicable for low quality and FFPE samples * Single-read sequencing of up to 9,216 samples/lane * Dual indexing and Unique Molecular Identifiers (UMIs) are available ### QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina The QuantSeq FWD Kit is a library preparation protocol designed to generate Illumina compatible libraries of sequences close to the 3’ end of polyadenylated RNA. QuantSeq FWD contains the Illumina Read 1 linker sequence in the second strand synthesis primer, hence NGS reads are generated towards the poly(A) tail, directly reflecting the mRNA sequence (see workflow). This version is the recommended standard for gene expression analysis. Lexogen furthermore provides a high-throughput version with optional dual indexing (i5 and i7 indices) allowing up to 9,216 samples to be multiplexed in one lane. #### Analysis of Low Input and Low Quality Samples The required input amount of total RNA is as low as 100 pg. QuantSeq is suitable to reproducibly generate libraries from low quality RNA, including FFPE samples. See Fig.1 and 2 for a comparison of two different RNA qualities (FFPE and fresh frozen cryo-block) of the same sample.  Figure 1 | Correlation of gene counts of FFPE and cryo samples.  Figure 2 | Venn diagrams of genes detected by QuantSeq at a uniform read depth of 2.5 M reads in FFPE and cryo samples with 1, 5, and 10 reads/gene thresholds. #### Mapping of Transcript End Sites By using longer reads QuantSeq FWD allows to exactly pinpoint the 3’ end of poly(A) RNA (see Fig. 3) and therefore obtain accurate information about the 3’ UTR.  Figure 3 | QuantSeq read coverage versus normalized transcript length of NGS libraries derived from FFPE-RNA (blue) and cryo-preserved RNA (red). ### Current workflow should be used only with the single-end RNA-Seq data. It performs the following steps: 1. Separates UMIes and trims adapters from input FASTQ file 2. Uses ```STAR``` to align reads from input FASTQ file according to the predefined reference indices; generates unsorted BAM file and alignment statistics file 3. Uses ```fastx_quality_stats``` to analyze input FASTQ file and generates quality statistics file 4. Uses ```samtools sort``` and generates coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 2 (after running STAR) 5. Uses ```umi_tools dedup``` and generates final filtered sorted BAM(+BAI) file pair 6. Generates BigWig file on the base of sorted BAM file 7. Maps input FASTQ file to predefined rRNA reference indices using ```bowtie``` to define the level of rRNA contamination; exports resulted statistics to file 8. Calculates isoform expression level for the sorted BAM file and GTF/TAB annotation file using GEEP reads-counting utility; exports results to file

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

Path: workflows/trim-quantseq-mrnaseq-se.cwl

Branch/Commit ID: 4360fb2e778ecee42e5f78f83b78c65ab3a2b1df