Workflow: GAT - Genomic Association Tester

Fetched 2023-01-09 00:52:10 GMT

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.

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Inputs

ID Type Title Doc
seed Integer (Optional) Number of random seed

Number of random seed
alias String Experiment short name/Alias
counter https://w3id.org/cwl/view/git/564156a9e1cc7c3679a926c479ba3ae133b1bfd4/workflows/gat-run.cwl#counter/counter (Optional) Set the measure of association to be tested

Set the measure of association to be tested

threads Integer (Optional) Number of threads

Number of threads for those steps that support multithreading
segment_file File [BED] Segments of interest (headerless TSV/CSV file with at least three columns: chr start end)

Headerless TSV/CSV file (at least 3 columns: chr start end) with sets of intervals whose association will be tested with annotation_file

workspace_file File [BED] Workspace (headerless TSV/CSV file with at least three columns: chr start end)

Headerless TSV/CSV file (at least 3 columns: chr start end) with genomic regions accessible for simulation

annotation_file File [BED] Annotations (headerless TSV/CSV file with at least three columns: chr start end)

Headerless TSV/CSV file (at least 3 columns: chr start end) with sets of intervals that are used for testing association of segment_file

permutations_count Integer (Optional) Number of random permutations

Number of random permutations

Steps

ID Runs Label Doc
run_gat
../tools/gat-run.cwl (CommandLineTool)

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.

Note: --ignore-segment-tracks parameter is hardcoded

prepare_report_file
../tools/custom-bash.cwl (CommandLineTool)

Tool to run custom script set as `script` input with arguments from `param`. Default script runs sed command over the input file and exports results to the file with the same name as input's basename

prepare_segment_file
../tools/custom-bash.cwl (CommandLineTool)

Tool to run custom script set as `script` input with arguments from `param`. Default script runs sed command over the input file and exports results to the file with the same name as input's basename

prepare_workspace_file
../tools/custom-bash.cwl (CommandLineTool)

Tool to run custom script set as `script` input with arguments from `param`. Default script runs sed command over the input file and exports results to the file with the same name as input's basename

prepare_annotation_file
../tools/custom-bash.cwl (CommandLineTool)

Tool to run custom script set as `script` input with arguments from `param`. Default script runs sed command over the input file and exports results to the file with the same name as input's basename

Outputs

ID Type Label Doc
gat_report File [TSV] Interval overlap statistics report

Interval overlap statistics report
gat_stderr_log File [Textual format] GAT stderr log

GAT stderr log
gat_stdout_log File [Textual format] GAT stdout log

GAT stdout log
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Permalink: https://w3id.org/cwl/view/git/564156a9e1cc7c3679a926c479ba3ae133b1bfd4/workflows/gat-run.cwl