Explore Workflows

https://github.com/PMCC-BioinformaticsCore/janis-pipelines.git

Path: janis_pipelines/wgs_somatic/cwl/tools/strelkaSomaticVariantCaller_v0_1_1.cwl

Branch/Commit ID: f7f887b84734a932534ed6a4732a48852e6169d4

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

Path: task_types/tt_fscr_calls_pass1.cwl

Branch/Commit ID: 0bc1c33a2293e054ad00974971edc79c13252cc7

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

Path: cwltool/schemas/v1.0/v1.0/count-lines1-wf.cwl

Branch/Commit ID: 203797516329f7fb8aa5e763e6f9b331c63c3060

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

Path: definitions/subworkflows/mutect.cwl

Branch/Commit ID: 3ee63d8757c341ca98b3b46ec4782862ad19b710

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

Path: task_types/tt_kmer_cache_store.cwl

Branch/Commit ID: 0bc1c33a2293e054ad00974971edc79c13252cc7

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

Path: definitions/pipelines/wgs.cwl

Branch/Commit ID: d2c2f2eb846ae2e9cdcab46e3bb88e42126cb3f5

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

Path: definitions/subworkflows/strelka_and_post_processing.cwl

Branch/Commit ID: a670f323e77e02d9b77be9a13d73d5276dd3676c

What is MAnorm? -------------- MAnorm is a robust model for quantitative comparison of ChIP-Seq data sets of TFs (transcription factors) or epigenetic modifications and you can use it for: * Normalization of two ChIP-seq samples * Quantitative comparison (differential analysis) of two ChIP-seq samples * Evaluating the overlap enrichment of the protein binding sites(peaks) * Elucidating underlying mechanisms of cell-type specific gene regulation How MAnorm works? ---------------- MAnorm uses common peaks of two samples as a reference to build the rescaling model for normalization, which is based on the empirical assumption that if a chromatin-associated protein has a substantial number of peaks shared in two conditions, the binding at these common regions will tend to be determined by similar mechanisms, and thus should exhibit similar global binding intensities across samples. The observed differences on common peaks are presumed to reflect the scaling relationship of ChIP-Seq signals between two samples, which can be applied to all peaks. What do the inputs mean? ---------------- ### General **Experiment short name/Alias** * short name for you experiment to identify among the others **ChIP-Seq SE sample 1** * previously analyzed ChIP-Seq single-read experiment to be used as Sample 1 **ChIP-Seq SE sample 2** * previously analyzed ChIP-Seq single-read experiment to be used as Sample 2 **Genome** * Reference genome to be used for gene assigning ### Advanced **Reads shift size for sample 1** * This value is used to shift reads towards 3' direction to determine the precise binding site. Set as half of the fragment length. Default 100 **Reads shift size for sample 2** * This value is used to shift reads towards 5' direction to determine the precise binding site. Set as half of the fragment length. Default 100 **M-value (log2-ratio) cutoff** * Absolute M-value (log2-ratio) cutoff to define biased (differential binding) peaks. Default: 1.0 **P-value cutoff** * P-value cutoff to define biased peaks. Default: 0.01 **Window size** * Window size to count reads and calculate read densities. 2000 is recommended for sharp histone marks like H3K4me3 and H3K27ac, and 1000 for TFs or DNase-seq. Default: 2000

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

Path: workflows/manorm-se.cwl

Branch/Commit ID: c5bae2ca862c764911b83d1f15ff6af4e2a0db28

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

Path: definitions/pipelines/germline_exome_gvcf.cwl

Branch/Commit ID: 7638b3075863ae8172f4adaec82fb2eb8e80d3d5

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

Path: tests/wf/mut2.cwl

Branch/Commit ID: 03af16c9df2ee77485d4ab092cd64ae096d2e71c