Experiment Config

The experiment config file has the following sections:

  1. [experiment]

  2. [sections]

  3. [reagents]

  4. [cycles]

  5. [filters]

  6. [method]

[experiment]

experiment details (required, unless noted)

  • method: name of installed method, path to method config file, or section name in config file

  • cycle: number of cycles to run (integer)

  • first flowcell: which flowcell to start first if running 2, optional (A or B)

[experiment]
method = 4i
cycles = 2
first flowcell = A

[sections]

position of sections on flowcell (required).

section name = AorB: LLx, LLy, URx, URy

  • section name: name/id of section to image (string)

  • AorB: flowcell section is on (A or B)

  • LLx: lower left x coordinate of section, use slide ruler (float)

  • LLy: lower left y coordinate of section, use slide ruler (float)

  • URx: upper right x coordinate of section, use slide ruler (float)

  • URy: upper right y coordinate of section, use slide ruler (float)

[sections]
section1 = A: 15.5, 45, 10.5, 35

[reagents]

Specify reagent ports (optional).

N = name

  • N: port number (integer)

  • Name: name of reagent (string)

[reagent]
6 = GFAP
7 = IBA1
8 = AF547 + Cy5

[cycles]

Specify cycle specific reagents (optional).

variablereagent N = name

  • variablereagent: cycle dependent reagent in recipe, specified in method config (string)

  • N: cycle (integer)

  • name: reagent used for variablereagent at cycle N (string)

[cycles]
1stab 1 = GFAP
1stab 2 = IBA1
2ndab 1 = AF547 + Cy5
2ndab 2 = AF547 + Cy5

[filters]

Specify cycle specific optical filters (optional).

lasercolor N = name

  • lasercolor: color of laser line, can use lower or uppercase initial (string)

  • N: cycle (integer)

  • name: optical density of filter to use (float/string), see table below.

laser color

laser index

filters (Optical Density)

green

1

open, 1.0, 2.0, 3.5, 3.8, 4.0, 4.5, home

red

2

open, 0.2, 0.5, 0.6, 1.0, 2.4, 4.0, home

 
[filters]
green 1 = 1.6
g 2 = 1.4
G 3 = 0.6
red 1 = 2.0
r 2 = 1.0
R 3 = 0.9

[method] in experiment config

Method specific HiSeq settings (optional)

Must match the method item in the [experiment] section. Instead of a method specific section in the experiment config file, a separate method config file may be used.

See [method] for details.

[4i]
recipe = 4i_recipe.txt