seismic pool

Purpose

seismic pool merges IDmut data from multiple samples into a single pooled sample. Use it when you sequenced the same RNA across multiple sequencing runs or libraries and want to analyze all reads together. The original samples are not modified; pool creates a new virtual sample that points to all of them.

Inputs

IDmut output directories or report files: One or more paths pointing to IDmut (or previously pooled) output. See Specify Input Files.
Pooled sample name: First positional argument: the name you want to give the new pooled sample.

Outputs

All outputs go into {out}/{pooled-sample}/idmut/{ref}/.

idmut-report.json: Pool report listing the names of all contributing samples. See Pool Report. This file is named idmut-report.json so that downstream steps (Filter, Table) accept it interchangeably with IDmut reports.

Quick example

Pool sample-1 and sample-2 into a sample named pooled:

seismic pool pooled out/sample-1/idmut out/sample-2/idmut

To pool every IDmut output in the output directory:

seismic pool pooled out/

Options

Quality filters

--min-pearson F: Skip pooling a pair of samples if their Pearson correlation is below F (default 0.0, i.e. no filter).
--max-marcd F: Skip pooling a pair of samples if their mean arcsine distance exceeds F (default 1.0, i.e. no filter).

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.

Common unexpected results

Warning: duplicate samples: An original sample appears more than once among the inputs (e.g. because you included both a sample and a pool that already contains it). Check the resulting pool report to confirm it contains what you expect.
Error: would overwrite existing non-pooled sample: You used a pooled sample name that already exists as a real sample. Choose a different name or remove the conflicting directory first.