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Graph Name Retrieved From View
workflow graph Motif Finding with HOMER with random background regions

Motif Finding with HOMER with random background regions --------------------------------------------------- HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. Here is how we generate background for Motifs Analysis ------------------------------------- 1. Take input file with regions in a form of “chr\" “start\" “end\" 2. Sort and remove duplicates from this regions file 3. Extend each region in 20Kb into both directions 4. Merge all overlapped extended regions 5. Subtract not extended regions from the extended ones 6. Randomly distribute not extended regions within the regions that we got as a result of the previous step 7. Get fasta file from these randomly distributed regions (from the previous step). Use it as background For more information please refer to: ------------------------------------- [Official documentation](http://homer.ucsd.edu/homer/motif/)

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

Path: workflows/homer-motif-analysis.cwl

Branch/Commit ID: 104059e07a2964673e21d371763e33c0afeb2d03
workflow graph predixcan.cwl

https://github.com/cwl-apps/predixcan_tools.git

Path: predixcan/predixcan.cwl

Branch/Commit ID: 5b49ef07b994963d190f4f508bc08e4bec8b8a0b
workflow graph exome alignment and germline variant detection

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

Path: definitions/subworkflows/germline_detect_variants.cwl

Branch/Commit ID: 1750cd5cc653f058f521b6195e3bec1e7df1a086
workflow graph ConcordanceCheckerWorkflow.cwl

https://github.com/DataBiosphere/topmed-workflows.git

Path: vcf-comparator/ConcordanceCheckerWorkflow.cwl

Branch/Commit ID: 0b86edf67a418240b576862d28c38d681c9cfa21
workflow graph SoupX - an R package for the estimation and removal of cell free mRNA contamination

Devel version of Single-Cell Advanced Cell Ranger Pipeline (SoupX) =================================================================

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

Path: workflows/soupx.cwl

Branch/Commit ID: 104059e07a2964673e21d371763e33c0afeb2d03
workflow graph BioExcel-CWL-firstWorkflow.cwl

https://github.com/bioexcel/biobb_wf_cwl_tutorial.git

Path: biobb_wf_cwl_tutorial/examples/BioExcel-CWL-firstWorkflow.cwl

Branch/Commit ID: 87b1378fdfd37bc4a232dae95486a1c4040c1505
workflow graph readgroup_fastq_pe.cwl

https://github.com/NCI-GDC/gdc-mirnaseq-cwl.git

Path: workflows/mirnaseq_automation/readgroup_fastq_pe.cwl

Branch/Commit ID: 963f6d502da2c4f152c1654e94008ccf8f6d0db3
workflow graph Exome QC workflow

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

Path: definitions/subworkflows/qc_exome.cwl

Branch/Commit ID: 1750cd5cc653f058f521b6195e3bec1e7df1a086
workflow graph Raw sequence data to BQSR

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

Path: definitions/subworkflows/sequence_to_bqsr.cwl

Branch/Commit ID: 1750cd5cc653f058f521b6195e3bec1e7df1a086
workflow graph Detect Docm variants

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

Path: definitions/subworkflows/docm_cle.cwl

Branch/Commit ID: 1750cd5cc653f058f521b6195e3bec1e7df1a086