Quick Start

This page shows minimal examples of running the ExSeq pipeline. For more information refer to the other wiki sections.

Minimal Usage:

• ./runPipeline.sh

This will run the pipeline pulling parameters (input directories, number of rounds etc.) from a file in the same directory named:

• loadParameters.m

The repository contains a template with annotated parameters with the most important ones described in the Parameters section.

Usage specifying command line parameters pulling unused parameters from the load parameters file.

• ./runPipeline.sh [OPTIONS]

The options which should be defined for most data sets are:

• -N number of rounds or '--auto-config' to calculate from files.
• -b file basename
• -I input image directory
• -O output directory containing folders described in Input Data Preparation.
• -L log directory

Optionally to run specific stages can use:

• -s to skip stages running all not listed
• -e to run only specific stages.

Either option can have a comma separated list of one or more of the following:

• setup-cluster, color-correction, normalization, registration, puncta-extraction, base-calling

For a full list of command line options use the refer to the options section or use the help option:

• -h

Examples

For these examples, assume we have a directory of input images, which are either direct from microscope or have been run through a deconvolution application, as follows.

/mp/nas1/share/ExSEQ/ExSeqSlice/input

We can either set this (or any other options shown) in a loadParameters.m file in the same directory but in this case we will specify this input directory with a command line option.

ex 1)

$ ./runPipeline.sh -I /mp/nas1/share/ExSEQ/ExSeqSlice/input --auto-config -b sa0916slicedncv

The number of rounds is set automatically from files in the input directory, and sets the file basename (project name) to sa0916slicedncv running all stages.

ex 2)

$ ./runPipeline.sh -I /mp/nas1/share/ExSEQ/ExSeqSlice/input --auto-config auto -b sa0916slicedncv -s setup-cluster,color-correction,normalization,registration,puncta-extraction

In addition to ex 1) parameters, we set to skip stages of most of the stages only running the base calling stage. We could have alternatively used the specific stage option like so:

• -e base-calling