Method Config

The method config file has 2 possible sections. Instead of a separate method config file, a method specific section in the experiment config file may be used (in which case only use 1 [reagent] section). See [method] in experiment config

[method]

HiSeq settings specific to the method.

The name of this section should match the name of the method. The only required key in this section is recipe. The other keys are optional.

  • recipe: path to the method recipe as its value (path), required

  • flush volume: volume to flush line with in uL (integer), default is 1000

  • main prime volume: volume to prime main lines (ports 1-8 & 10-19) in uL (integer), default is 500

  • side prime volume: volume to prime side lines (ports 9 & 22-24) in uL (integer), default is 350

  • sample prime volume: volume to prime samples lines (port 20) in uL (integer), default is 250

  • flush speed: flowrate to flush lines with in uL/min (integer), default is 700

  • reagent speed: flowrate to pump reagents during recipe in uL/min (integer), default is the minimum flow rate

  • variable reagents: name of variable ports in recipes that are cycle dependent (string)

  • first port: port to start recipe at on first cycle (string)

  • barrels per lane: number of syringe barrels that are used per lane on flowcell (integer), default is 8

  • inlet ports: 2 inlet port row or 8 inlet port row (integer), default is 2

  • laser power: set power of laser in mW (integer), default is 10

  • z position: step of tilt motors when imaging (integer), default is 21500

  • focus filter 1: filter for green laser for autofocus routine, default is 2.0

  • focus filter 2: filter for red laser for autofocus routine, default is 2.0

  • default em filter: emission filter used for imaging, True for in path, False for out of path (bool), default is True

  • default filter 1: filter for green laser if not specified in [filter] section of experiment config file (float/string), default is home

  • default filter 2: filter for red laser if not specified in [filter] section of experiment config file (float/string), default is home

  • rinse: reagent to rinse the flowcell with between completion of the experiment and flushing of the lines during shutdown (string), default is None

  • autofocus: routine used for autofocusing (string), see Autofocus for more info, default is partial once

  • focus tolerance: distance in microns for acceptable focus error, default is 0 um which allows for maximum error

  • enable z stage: Enable/disable z stage movements (bool), default is True.

  • bundle height: sensor bundle height of cameras (integer), only certain values are valid, default is 128

  • temperature interval: time between checking temperature of flowcell (integer), default is 5

    [4i]
recipe = 4i_recipe.txt
flush speed = 500
flush volume = 1000
reagent speed = 200
variable reagents = 1stab, 2ndab
first port = blocking
barrels per lane = 8
laser power = 400

[reagents] in method config

Specify ports for reagent specific to the method. This is useful if running a method repeatedly and none or some of the ports change from each experiment. Alternatively, all the ports may be specified in the experiment config.

See [reagents] for details.