seismic clusterscan

Purpose

seismic clusterscan clusters the domains that seismic filterscan detected along an RNA. It runs the cluster step on each domain separately, inferring how many alternative structures (clusters) that domain folds into and the proportion of reads in each. Use it after seismic filterscan to resolve the structural heterogeneity within each data-driven domain.

Inputs

Filterscan output directory or report file: One or more filterscan output directories or filterscan-report.json files. See Specify Input Files for ways to select multiple inputs at once.

Outputs

All outputs go into {out}/{sample}/clusterscan/{ref}/{reg}/.

clusterscan-report.json: Summary of the run, including the best number of clusters for each domain. See Clusterscan Report.

The cluster step is also run on each domain, producing the same output as seismic cluster for every domain.

Quick example

Cluster the domains that filterscan found:

seismic clusterscan out/sample-1/filterscan/long-rna

Options

Cluster options

All seismic cluster options are accepted and applied to each domain, such as --min-clusters/--max-clusters to bound the number of clusters and the various run-quality filters.

Branches

--branch X (-b): Create a new branch: output results in {out}/{sample}/clusterscan_{branch}. See Branches.

Performance

--num-cpus N — multiprocessing; see Parallelize Tasks. --force — overwrite existing outputs.

The auto-generated Command Line Reference lists every option with its current default.