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== | ==Genome Analyzer User Guide== | ||
== | ==SCS v2.4== | ||
*start up scsv2.4 | |||
* | ===setting the run parameters=== | ||
*click <view> | |||
*clear box next to show on start up | |||
*from the data collection screen | |||
*edit|run parameters|GA Settings / RunBrowser Settings | |||
===GA Setting=== | |||
*specify the network location for run results | |||
*set perferences for real time analysis results | |||
*set settings for auto calibration | |||
*delete images (select this option to delete images from the genome analyzer computer after analysis | |||
====Validation strings==== | |||
*edit if you are using a customized identification system | |||
====Use auto calibration==== | |||
*select this option to enable the auto calibration feature | |||
*refer to page 29 for a description of the auto calibration feature | |||
*note: if this option is cleared, focus calibration must be performed manually as described in appendix B | |||
* | |||
===Run Browser Settings=== | |||
*runbrowzer reports, specify which runbrowser reports you want to show and export | |||
if selected the first cycle is generated by the software | |||
*enable runbrowser report emails to sens reports to the email addresses specified | |||
*after you have finished selecting the settings in the run parameters window, click <save & continue>/<cancel & continue>/<reset default configs> | |||
== | ===initialize the software=== | ||
*click the manual control/setup tab | |||
*perform any operation to trigger the genome analyzer initialization | |||
* | |||
== | ===run window=== | ||
====recipe tab==== | |||
*hover over a stop to show the parameters specific to that step | |||
====image cycletab==== | |||
white tile are queued for imaging | |||
blue tiles haven been imaged | |||
gray tiles are not defined in the current run | |||
right side of the window shows the photographs being taken of the current tile | |||
== | ====temperature tab==== | ||
*for monitor various run temperatures | |||
* | |||
== | ===manual control/setup window=== | ||
* | ====manual control==== | ||
* | *settings used for manual focus calibration | ||
====pump tab==== | |||
command | |||
to | |||
solution | |||
volume(ml) | |||
aspirate rate(ml/min) | |||
dispense rate(ml/min) | |||
====recipe viewer==== | |||
*genome analyzer recipes found can be found in | |||
<install directory>\datacollection_v<#>\bin\recipes | |||
*to access the recipe view click file|open recipe from the toolbar | |||
*the following information is listed for each recipe | |||
recipe | |||
subfolder | |||
cycle | |||
read end | |||
multiplexing | |||
service | |||
version | |||
comment | |||
file status | |||
====editing cycle number==== | |||
*click edit on the recipe viewer toolbar | |||
===reagent tracking=== | |||
*provides email notifications and warnings when reagents are getting low and need replacing | |||
*beneficial when performing runs longer than 36 cycles | |||
*click reagents from the toolbar at the top of the data collection software screen | |||
====current volumes==== | |||
== | ====reset volumes==== | ||
====reagent barcodes==== | |||
*to track reagents for any given run | |||
barcodes are stored in the Reagentsld.xml file in the runfolder | |||
*if the remaining reagents are not to be used click clear | |||
====configure tracking==== | |||
*to enable or disable reagent tracking features select reagents|configure tacking | |||
enable volume tracking | |||
autostop when empty | |||
display and email warnings | |||
===disk space checking=== | |||
*during the run at the end of each cycle the software checks available disk space | |||
*if there is insufficient disk space to accommodate one cycle the software pauses the run and a dialog box appears to tell you how much dish space remains. when sufficient disk space is available the dialog box closes and the run automatically resumes | |||
===image control=== | |||
zoom in | |||
move the zoomed image | |||
zoom out | |||
modify the color display | |||
view or hide the center mark | |||
see intensity values | |||
see focus quality and uniformity | |||
show region of interest | |||
save the image | |||
==run folders== | |||
*each run on the genome analyzer generates a run folder that contains data files and log files specific for that run | |||
*when you start a run the software prompts you to enter the folder name for it | |||
by default the folder is named YYMMDD_<Workstation Name>_<Run #> | |||
*the run folder name may not contain any spaces | |||
====run folder path==== | |||
*the name and location of this folder are set in <install location>\bin\config\rcmconfig in this line | |||
<Run Path="D:\Runs" /> | |||
* to change the run folder path wither change this line or select run|select run folder root in the software | |||
==Cluster Station== | |||
==GA Pipeline 1.4== | |||
*[[Media: Pipeline_CASAVA_User_Guide_15003807_A.pdf|Manual]] |
Latest revision as of 02:48, 24 July 2009
Genome Analyzer User Guide[edit]
SCS v2.4[edit]
- start up scsv2.4
setting the run parameters[edit]
- click <view>
- clear box next to show on start up
- from the data collection screen
- edit|run parameters|GA Settings / RunBrowser Settings
GA Setting[edit]
- specify the network location for run results
- set perferences for real time analysis results
- set settings for auto calibration
*delete images (select this option to delete images from the genome analyzer computer after analysis
Validation strings[edit]
- edit if you are using a customized identification system
Use auto calibration[edit]
- select this option to enable the auto calibration feature
- refer to page 29 for a description of the auto calibration feature
- note: if this option is cleared, focus calibration must be performed manually as described in appendix B
Run Browser Settings[edit]
- runbrowzer reports, specify which runbrowser reports you want to show and export
if selected the first cycle is generated by the software
- enable runbrowser report emails to sens reports to the email addresses specified
- after you have finished selecting the settings in the run parameters window, click <save & continue>/<cancel & continue>/<reset default configs>
initialize the software[edit]
- click the manual control/setup tab
- perform any operation to trigger the genome analyzer initialization
run window[edit]
recipe tab[edit]
- hover over a stop to show the parameters specific to that step
image cycletab[edit]
white tile are queued for imaging blue tiles haven been imaged gray tiles are not defined in the current run right side of the window shows the photographs being taken of the current tile
temperature tab[edit]
- for monitor various run temperatures
manual control/setup window[edit]
manual control[edit]
- settings used for manual focus calibration
pump tab[edit]
command to solution volume(ml) aspirate rate(ml/min) dispense rate(ml/min)
recipe viewer[edit]
- genome analyzer recipes found can be found in
<install directory>\datacollection_v<#>\bin\recipes
- to access the recipe view click file|open recipe from the toolbar
- the following information is listed for each recipe
recipe subfolder cycle read end multiplexing service version comment file status
editing cycle number[edit]
- click edit on the recipe viewer toolbar
reagent tracking[edit]
- provides email notifications and warnings when reagents are getting low and need replacing
- beneficial when performing runs longer than 36 cycles
- click reagents from the toolbar at the top of the data collection software screen
current volumes[edit]
reset volumes[edit]
reagent barcodes[edit]
- to track reagents for any given run
barcodes are stored in the Reagentsld.xml file in the runfolder
- if the remaining reagents are not to be used click clear
configure tracking[edit]
- to enable or disable reagent tracking features select reagents|configure tacking
enable volume tracking autostop when empty display and email warnings
disk space checking[edit]
- during the run at the end of each cycle the software checks available disk space
- if there is insufficient disk space to accommodate one cycle the software pauses the run and a dialog box appears to tell you how much dish space remains. when sufficient disk space is available the dialog box closes and the run automatically resumes
image control[edit]
zoom in move the zoomed image zoom out modify the color display view or hide the center mark see intensity values see focus quality and uniformity show region of interest save the image
run folders[edit]
- each run on the genome analyzer generates a run folder that contains data files and log files specific for that run
- when you start a run the software prompts you to enter the folder name for it
by default the folder is named YYMMDD_<Workstation Name>_<Run #>
- the run folder name may not contain any spaces
run folder path[edit]
- the name and location of this folder are set in <install location>\bin\config\rcmconfig in this line
<Run Path="D:\Runs" />
- to change the run folder path wither change this line or select run|select run folder root in the software