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 loadParameters.m file in the same directory. The repository contains a template for full description see the Parameters section.

Usage specifying command line parameters that should be set if not in loadParameters.m or not using that file: ./runPipeline [OPTIONS]

The other options should be:

• -N number of rounds or '--auto-config' to calculate from files.
• -b file basename
• -c channel names; e.g. " 'ch01', 'ch02', 'ch03', 'ch04' "
• -I input image directory
• -O output directory
• -L log directory optionally -s to skip stages or -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 -h help option or refer to the options section.

For example, 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 -c "'chan1','chan2','chan3','chan4'"

We set automatically the number of rounds from files in deconvolution directory, set file basename (project name) to 'sa0916slicedncv', and set channel names to 'chan1','chan2','chan3','chan4', each of which has to be enclosed with single quotation mark.

ex 2)

$ ./runPipeline.sh -I /mp/nas1/share/ExSEQ/ExSeqSlice/input --auto-config auto -b sa0916slicedncv -c "'chan1','chan2','chan3','chan4'" -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 -e base-calling).