Explore Workflows

https://git.astron.nl/eosc/prefactor3-cwl.git

Path: workflows/HBA_target.cwl

Branch/Commit ID: 6633c39d59a81b9ebf8312450bf50d6a0fe66efa

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

Path: definitions/subworkflows/pindel_region.cwl

Branch/Commit ID: a08de598edc04f340fdbff76c9a92336a7702022

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

Path: structuralvariants/workflow.cwl

Branch/Commit ID: 0864e19de6a1732a1376c6a64a93794d2fc45d23

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: 104059e07a2964673e21d371763e33c0afeb2d03

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

Path: definitions/pipelines/germline_wgs.cwl

Branch/Commit ID: a08de598edc04f340fdbff76c9a92336a7702022

Both `islands_file` and `islands_control_file` should be produced by the same cwl tool (iaintersect.cwl or macs2-callpeak-biowardrobe-only.cwl)

https://github.com/Barski-lab/workflows.git

Path: workflows/super-enhancer.cwl

Branch/Commit ID: bc75349ad3a7bdce82b4cd8584501f4d0280bb8d

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

Path: task_types/tt_ani_top_n.cwl

Branch/Commit ID: e3f18c61d1bbf65e40921dbd044369da4523ee3e

https://github.com/NAL-i5K/Organism_Onboarding.git

Path: final-workflow.cwl

Branch/Commit ID: 89cff9f0d36a23bf57b3f4bdbd3ed57e3347c945

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

Path: definitions/pipelines/alignment_exome_nonhuman.cwl

Branch/Commit ID: 7638b3075863ae8172f4adaec82fb2eb8e80d3d5

Pairwise comparison

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

Path: task_types/tt_kmer_compare_wnode.cwl

Branch/Commit ID: d39017c63dd8e088f1ad3809d709529df602e05f