Explore Workflows

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

Path: definitions/subworkflows/qc_wgs.cwl

Branch/Commit ID: 889a077a20c0fdb01f4ed97aa4bc40f920c37a1a

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

Path: workflows/emg-pipeline-v3.cwl

Branch/Commit ID: 316831663e84623eb0e3a260af252fef441924d4

https://github.com/pitagora-network/DAT2-cwl.git

Path: workflow/rna-seq/rnaseq-star-rsem-pe/rnaseq-star-rsem-pe.cwl

Branch/Commit ID: 69e7c0479af00695127e402962e1d81b6b8142df

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

Path: definitions/pipelines/downsample_and_recall.cwl

Branch/Commit ID: 889a077a20c0fdb01f4ed97aa4bc40f920c37a1a

https://github.com/nci-gdc/gdc-dnaseq-cwl.git

Path: workflows/bamfastq_align/readgroup_fastq_se.cwl

Branch/Commit ID: 0495e3095182b2e1b4d6274833b3d2ce30347a4e

SoupX Estimate ==============

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

Path: workflows/soupx.cwl

Branch/Commit ID: 581156366f91861bd4dbb5bcb59f67d468b32af3

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

Path: definitions/pipelines/alignment_wgs.cwl

Branch/Commit ID: 97572e3a088d79f6a4166385f79e79ea77b11470

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: 581156366f91861bd4dbb5bcb59f67d468b32af3

https://github.com/pitagora-network/DAT2-cwl.git

Path: workflow/epigenome-chip-seq/epigenome-chip-seq.packed.cwl

Branch/Commit ID: 0cd20e1be620ae0817a1aa4286d73b78c89809f0

Packed ID: macs2.cwl

Workflow pilon assembly polishing Steps: - BBmap (Read mapping to assembly) - Pilon

https://git.wur.nl/unlock/cwl.git

Path: cwl/workflows/workflow_pilon_mapping.cwl

Branch/Commit ID: 60fafdfbec9b39c860945ef4634e0c28cb5e976c