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GAT: Genomic Association Tester ============================================== A common question in genomic analysis is whether two sets of genomic intervals overlap significantly. This question arises, for example, in the interpretation of ChIP-Seq or RNA-Seq data. The Genomic Association Tester (GAT) is a tool for computing the significance of overlap between multiple sets of genomic intervals. GAT estimates significance based on simulation. Gat implemements a sampling algorithm. Given a chromosome (workspace) and segments of interest, for example from a ChIP-Seq experiment, gat creates randomized version of the segments of interest falling into the workspace. These sampled segments are then compared to existing genomic annotations. The sampling method is conceptually simple. Randomized samples of the segments of interest are created in a two-step procedure. Firstly, a segment size is selected from to same size distribution as the original segments of interest. Secondly, a random position is assigned to the segment. The sampling stops when exactly the same number of nucleotides have been sampled. To improve the speed of sampling, segment overlap is not resolved until the very end of the sampling procedure. Conflicts are then resolved by randomly removing and re-sampling segments until a covering set has been achieved. Because the size of randomized segments is derived from the observed segment size distribution of the segments of interest, the actual segment sizes in the sampled segments are usually not exactly identical to the ones in the segments of interest. This is in contrast to a sampling method that permutes segment positions within the workspace.

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

Path: workflows/gat-run.cwl

Branch/Commit ID: 2c486543c335bb99b245dfe7e2f033f535efb9cf

RNAs - qc, preprocess, annotation, index, abundance

https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/amplicon-fastq.workflow.cwl

Branch/Commit ID: 662d424d2e433e636f46a79025325d5daaca6271

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

Path: task_types/tt_univec_wnode.cwl

Branch/Commit ID: 1bf7dc7b03ea3c64e54375cc5c3767849a801000

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

Path: task_types/tt_kmer_top_n_extract.cwl

Branch/Commit ID: a34f47d1e37af51e387ecdfa5c3047f106c1146b

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

Path: definitions/subworkflows/umi_alignment.cwl

Branch/Commit ID: 441b85003fdc10cf4cbf333d89acb4d23b0fef32

Workflow runs [STAR](https://github.com/alexdobin/STAR) v2.5.3a (03/17/2017) PMID: [23104886](https://www.ncbi.nlm.nih.gov/pubmed/23104886) to build indices for reference genome provided in a single FASTA file as fasta_file input and GTF annotation file from annotation_gtf_file input. Generated indices are saved in a folder with the name that corresponds to the input genome.

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

Path: workflows/star-index.cwl

Branch/Commit ID: 2c486543c335bb99b245dfe7e2f033f535efb9cf

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

Path: task_types/tt_fscr_calls_pass1.cwl

Branch/Commit ID: bba6c580ab88e077f6aa2c2ee7c73159f3f9156e

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

Path: task_types/tt_kmer_cache_retrieve.cwl

Branch/Commit ID: 7319ccfd2108929588bdc266d9df198629dfaa65

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

Path: task_types/tt_blastn_wnode.cwl

Branch/Commit ID: 7319ccfd2108929588bdc266d9df198629dfaa65

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

Path: tests/wf/mut2.cwl

Branch/Commit ID: fec7a10466a26e376b14181a88734983cfb1b8cb