Explore Workflows

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: 480e99a4bb3046e0565113d9dca294e0895d3b0c

https://github.com/common-workflow-lab/wdl-cwl-translator.git

Path: wdl2cwl/tests/cwl_files/workflow_inputs.cwl

Branch/Commit ID: 0e2aa9ed4acb6a14ca5722e81b2eb4bfb303e153

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

Path: definitions/subworkflows/hs_metrics.cwl

Branch/Commit ID: 6949082038c1ad36d6e9848b97a2537aef2d3805

This workflow takes in single-end reads, and performs the following steps in order: demux_se.cwl (does not actually demux for single end, but mirrors the paired-end processing protocol)

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

Path: cwl/wf_demultiplex_se.cwl

Branch/Commit ID: b2b95f58f96ee5b34bd9b342d0ecda63d135e278

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

Path: definitions/subworkflows/umi_alignment.cwl

Branch/Commit ID: 788bdc99c1d5b6ee7c431c3c011eb30d385c1370

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

Path: flow_dispatch/2other_species/workflow.cwl

Branch/Commit ID: aa375dcaa5ccfbb4e2aa4433d10948c641b044eb

https://github.com/common-workflow-lab/wdl-cwl-translator.git

Path: wdl2cwl/tests/cwl_files/align_and_count.cwl

Branch/Commit ID: 0e2aa9ed4acb6a14ca5722e81b2eb4bfb303e153

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

Path: task_types/tt_cache_asnb_entries.cwl

Branch/Commit ID: 5e92165ac2c11608ab2db42fe2d66eabe72dbb40

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

Path: tests/wf/1st-workflow.cwl

Branch/Commit ID: 1441c285e8a5afe399f5d52ca9059cb8bb513edb

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

Path: definitions/subworkflows/fastq_to_bqsr.cwl

Branch/Commit ID: 6b365b79675b2aabfb8d5829bb8df0a6e986b037