Explore Workflows

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

Path: task_types/tt_format_rrnas_from_seq_entry.cwl

Branch/Commit ID: 2801ce53744a085580a8de91cd007c45146b51e8

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

Path: cwltool/schemas/v1.0/v1.0/count-lines6-wf.cwl

Branch/Commit ID: e9c83739a93fa0b18f8dea2f98b632a9e32725c9

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

Path: definitions/subworkflows/docm_germline.cwl

Branch/Commit ID: 51724b44c96e5fd849ae55b752865b80bc47d66c

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: c5bae2ca862c764911b83d1f15ff6af4e2a0db28

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

Path: definitions/subworkflows/gatk_haplotypecaller_iterator.cwl

Branch/Commit ID: e59c77629936fad069007ba642cad49fef7ad29f

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

Path: tests/wf-loadContents2.cwl

Branch/Commit ID: c7c97715b400ff2194aa29fc211d3401cea3a9bf

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

Path: definitions/subworkflows/sequence_to_bqsr_nonhuman.cwl

Branch/Commit ID: da335d9963418f7bedd84cb2791a0df1b3165ffe

Runs RNA-Seq BioWardrobe basic analysis with single-end data file.

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

Path: workflows/trim-rnaseq-se.cwl

Branch/Commit ID: 4b8bb1a1ec39056253ca8eee976078e51f4a954e

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

Path: tests/sum-wf-noET.cwl

Branch/Commit ID: ea9f8634e41824ac3f81c3dde698d5f0eef54f1b

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

Path: task_types/tt_blastp_wnode_struct.cwl

Branch/Commit ID: e3f18c61d1bbf65e40921dbd044369da4523ee3e