Explore Workflows

Quality Control (raw data), Raw Data trimming and Quality Control (pre-processed)

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/subworkflows/trimmed_fastq.cwl

Branch/Commit ID: 992f84a959e1776acf3be77d2ca15fe11fa8673d

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

Path: definitions/subworkflows/qc_wgs.cwl

Branch/Commit ID: 641083e9ed933d388f36fa04c00c20a810599e94

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

Path: task_types/tt_align_sort_sa.cwl

Branch/Commit ID: 205f4ceb47ba7537a6923d2dfb03668317c2fd89

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

Path: definitions/pipelines/detect_variants_wgs.cwl

Branch/Commit ID: f615832615c3b41728df8e47b72ef11e37e6a9e5

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

Path: testdata/stdout-wf_v1_2.cwl

Branch/Commit ID: 141048ae4b78aa765782bb752be4a1550edc2eea

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 PE sample 1** * previously analyzed ChIP-Seq paired-end experiment to be used as Sample 1 **ChIP-Seq PE sample 2** * previously analyzed ChIP-Seq paired-end 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-pe.cwl

Branch/Commit ID: cbefc215d8286447620664fb47076ba5d81aa47f

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

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf6.cwl

Branch/Commit ID: 814bd0405a7701efc7d63e8f0179df394c7766f7

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: d8a8af9fdb69c0a4003680c1d3b96f35d5e48f0e

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

Path: task_types/tt_cache_asnb_entries.cwl

Branch/Commit ID: ef266744578e2dcbce57c110c6fa3b9eee91e316

a workflow that performs grep followed by sort

https://github.com/ResearchObject/runcrate.git

Path: tests/data/grepsort-run-1/snapshot/grepsort.cwl

Branch/Commit ID: 9e40a51a9e48239bbd5fb5d3b6c4a8ef32e8169b