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 will run the pipeline pulling parameters from a loadParameters.m file in the same directory (repository contains a template for full description see the [Parameters](https://github.com/dgoodwin208/ExSeqProcessing/wiki/Parameters section).

Usage specifying command line parameters that should be set if not in loadParameters.m or not using that file: ./runPipeline [OPTIONS] either -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 setup-cluster,color-correction,normalization,registration,puncta-extraction,base-calling.

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

/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 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 use -e base-calling).