Explore Workflows

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

Path: structuralvariants/cwl/subworkflows/indexing_bed.cwl

Branch/Commit ID: f4c51a054b1ec51d07d89c6a8218e610653675f3

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: 7030da528559c7106d156284e50ff0ecedab0c4e

https://github.com/EBI-Metagenomics/pipeline-v5.git

Path: workflows/subworkflows/seqprep-subwf.cwl

Branch/Commit ID: 6ec8d032feb120eb0eebf9a0c01d48deabf42eea

https://github.com/EBI-Metagenomics/pipeline-v5.git

Path: workflows/subworkflows/amplicon/trim_and_reformat_reads.cwl

Branch/Commit ID: 6ec8d032feb120eb0eebf9a0c01d48deabf42eea

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

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf3.cwl

Branch/Commit ID: 665141f319e6b23bd9924b14844f2e979f141944

Packed ID: main

https://github.com/EBI-Metagenomics/pipeline-v5.git

Path: workflows/subworkflows/cmsearch-multimodel-raw-data.cwl

Branch/Commit ID: 6ec8d032feb120eb0eebf9a0c01d48deabf42eea

https://github.com/EBI-Metagenomics/pipeline-v5.git

Path: workflows/conditionals/amplicon/amplicon-1.cwl

Branch/Commit ID: 6ec8d032feb120eb0eebf9a0c01d48deabf42eea

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

Path: definitions/subworkflows/varscan_pre_and_post_processing.cwl

Branch/Commit ID: 0d2f354af9192a56af258a7d2426c7c160f4ec1a

ChIP-seq 02 trimming - reads: PE

https://github.com/Duke-GCB/GGR-cwl.git

Path: v1.0/ChIP-seq_pipeline/02-trim-pe.cwl

Branch/Commit ID: 6e68bda2cb45e8dc8e4d067c4220d65acfa53065

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

Path: definitions/subworkflows/filter_vcf.cwl

Branch/Commit ID: 0d2f354af9192a56af258a7d2426c7c160f4ec1a