Explore Workflows

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: 42dc4f70b117e78785b82865ec4c4b941ac1c259

https://github.com/mscheremetjew/workflow-is-cwl.git

Path: workflows/phmmer-v3.2-chunked-wf.cwl

Branch/Commit ID: 72bbd5a80688e6a387bfdff5881db2cc3523f7b7

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

Path: src/_includes/cwl/workflows/nestedworkflows.cwl

Branch/Commit ID: 3bfa62397cece91175f3652e2df7d8b43beb0c15

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

Path: src/_includes/cwl/workflows/1st-workflow.cwl

Branch/Commit ID: 3bfa62397cece91175f3652e2df7d8b43beb0c15

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/wf-loadContents2.cwl

Branch/Commit ID: 5f27e234b4ca88ed1280dedf9e3391a01de12912

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/count-lines11-null-step-wf.cwl

Branch/Commit ID: 57baec040c99d7edef8242ef51b5470b1c82d733

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

Path: definitions/subworkflows/duplex_alignment.cwl

Branch/Commit ID: 31a179d7a2f2ac86bfd7fcc4dc79832c3739ae76

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

Path: tests/wf/mut.cwl

Branch/Commit ID: e8b3565a008d95859fc44227987a54e6a53a8c29

https://github.com/tmooney/cancer-genomics-workflow.git

Path: definitions/subworkflows/molecular_qc.cwl

Branch/Commit ID: 0db1a5f1ceedd4416ac550787c27b99c87dbe985

Workflow converts input BAM file into bigWig and bedGraph files. Input BAM file should be sorted by coordinates (required by `bam_to_bedgraph` step). If `split` input is not provided use true by default. Default logic is implemented in `valueFrom` field of `split` input inside `bam_to_bedgraph` step to avoid possible bug in cwltool with setting default values for workflow inputs. `scale` has higher priority over the `mapped_reads_number`. The last one is used to calculate `-scale` parameter for `bedtools genomecov` (step `bam_to_bedgraph`) only in a case when input `scale` is not provided. All logic is implemented inside `bedtools-genomecov.cwl`. `bigwig_filename` defines the output name only for generated bigWig file. `bedgraph_filename` defines the output name for generated bedGraph file and can influence on generated bigWig filename in case when `bigwig_filename` is not provided. All workflow inputs and outputs don't have `format` field to avoid format incompatibility errors when workflow is used as subworkflow.

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

Path: tools/bam-bedgraph-bigwig.cwl

Branch/Commit ID: 42dc4f70b117e78785b82865ec4c4b941ac1c259