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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: a1f6ca50fcb0881781b3ba0306dd61ebf555eaba

https://github.com/Duke-GCB/bespin-cwl.git

Path: subworkflows/exomeseq-gatk4-02-variantdiscovery.cwl

Branch/Commit ID: 9f96a6621a0925d4a1ef4b6a733316149520b008

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

Path: definitions/subworkflows/gatk_haplotypecaller_iterator.cwl

Branch/Commit ID: 049f4aeff4c4a1b8421cac9b1c1c1f0da5848315

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

Path: task_types/tt_kmer_build_tree.cwl

Branch/Commit ID: 485f0be56cea77bff62b797ae7eff422a990a92c

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

Path: task_types/tt_bact_get_kmer_reference.cwl

Branch/Commit ID: e71779665f42fcf34601b0f65e030bb0dd47fa79

https://github.com/YeoLab/eclip.git

Path: cwl/wf_get_peaks_nostats_se.cwl

Branch/Commit ID: c0fffc4979a92371dc0667a03e3d957bf7f77600

Vegetation index processor, the greatest

https://github.com/EOEPCA/app-vegetation-index.git

Path: vegetation-index.cwl

Branch/Commit ID: dbf6e6e9da00019b0c4f7e497da59e68ba955486

Packed ID: vegetation-index

CNV CODEX calling

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

Path: structuralvariants/cwl/subworkflows/cnv_codex.cwl

Branch/Commit ID: f4c51a054b1ec51d07d89c6a8218e610653675f3

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

Path: definitions/subworkflows/varscan.cwl

Branch/Commit ID: 258bd4353ad1ca7790b3ae626bf42ab8194e7561

This is a subworkflow of the main oxog_varbam_annotat_wf workflow - this is not meant to be run as a stand-alone workflow!

https://github.com/david4096/OxoG-Dockstore-Tools.git

Path: annotator_sub_wf.cwl

Branch/Commit ID: 6366ed398da10019b6d81a789291af6d909f28f4