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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: e45ab1b9ac5c9b99fdf7b3b1be396dc42c2c9620
workflow graph RNASelector as a CWL workflow

https://doi.org/10.1007/s12275-011-1213-z

 https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl.git

Path: workflows/rna-selector.cwl

Branch/Commit ID: ecf044f3a5a7589cb2238487a19f22863c2bcdb1
workflow graph Subworkflow to allow calling different SV callers which require bam files as inputs

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

Path: definitions/subworkflows/single_sample_sv_callers.cwl

Branch/Commit ID: 2decd55996b912feb48be5db1b052aa3274ee405
workflow graph align_merge_sas

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

Path: task_types/tt_align_merge_sas.cwl

Branch/Commit ID: a402541b8530f30eab726c160da90a23036847a1
workflow graph kmer_top_n_extract

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

Path: task_types/tt_kmer_top_n_extract.cwl

Branch/Commit ID: a402541b8530f30eab726c160da90a23036847a1
workflow graph taxonomy_check_16S

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

Path: task_types/tt_taxonomy_check_16S.cwl

Branch/Commit ID: 6ac47e5703d8c8cdac698de91143829b3911e9b2
workflow graph kmer_build_tree

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

Path: task_types/tt_kmer_build_tree.cwl

Branch/Commit ID: a79cec2331b3e17e382e8e5040405e8dd750c639
workflow graph Merge, annotate, and generate a TSV for SVs

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

Path: definitions/subworkflows/merge_svs.cwl

Branch/Commit ID: 2decd55996b912feb48be5db1b052aa3274ee405
workflow graph tt_fscr_calls_pass1

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

Path: task_types/tt_fscr_calls_pass1.cwl

Branch/Commit ID: 4e2a295bb6c8b4982402ee80538a0cdb8ee6b6dd
workflow graph Filter single sample sv vcf from depth callers(cnvkit/cnvnator)

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

Path: definitions/subworkflows/sv_depth_caller_filter.cwl

Branch/Commit ID: 2decd55996b912feb48be5db1b052aa3274ee405