How to roll your own FCS files

*updated 2/18/2010*
- added a new section with demo file, video tutorial and some comments at the bottom *

This recipe will allow you to convert non-FCS database tables into FCS files for use with FlowJo software.

The data file MUST have EXACTLY the following format. Each line is delimited by a carriage return .

Line 1: FJTEXTDATA
Line 2: Number of key / value pairs ( = "nKeys")
Lines 3 ... nKyes + 2: KeywordName KeywordValue

Remaining lines contain tab-delimited channel values for each set of parameters for each event

The following keywords must be included:

$Fil
$Tot
$PnN, $PnR, $PnS, $PnB (set to 16), $PnR, $PnG, $PnE [for each parameter]
$Mode (must have a value "L")

For example:

FJTEXTDATA
16
$TOT 2
$FIL thisFile.txt
$PAR 2
$P1R 1024
$P1S stain 1
$P1N P1
$P1B 16
$P1G 1
$P1L 0.1, 4
$P2R 1024
$P2S stain 2
$P2N P2
$P2B 16
$P2G 1
$P2E 0.1, 4
$Mode L
312 456
123 222

Here is a video walk thru of the process:
Download Roll_your_own_FCS

Here is a sample text file I was showing the spreadsheet of in the video:
Download Test_fjtextdata

Here is what it should look like once loaded into FlowJo:

Comments

[David]

hi, I tried the above (cut and pasted the example text into notepad and saved as "thisFile.txt") and it doesn't work. I am using FlowJo ver 7.2.5
Any ideas?
thanks
David

[Maciej Simm]

Hi, David,

this trick is for the Mac version. It hasn't occurred to me to put this feature on the PC version - I'll try to push for including this in 7.5 release.

[Peter J Buontempo]

I also tried this (cut and pasted the example text into word and saved as "thisFile.txt") and it doesn't work. Is there any trick to what type of text file format to save it in?
I am using FlowJo ver 8.7.1 on Leopard
Any ideas, I am trying to analyze high content data with flow jo ?
thanks
Pete

[maciej simm]

I believe cut/paste from the blog above may convert some of the tabs to spaces. Please search for "space" and replace with "tab" (or do it manually :) ). The result should yield a two-event file.

ms

[maciej simm]

worth noting -

I've created a much easier utility to convert text into FCS files. see it here - http://flowjo.typepad.com/the_daily_dongle/2010/12/roll-your-own-fcs-files-part-2.html#more

ms

[Jeff]

I like the "roll your own" reference. Keep up being and awesome company! Cheers from Seattle!

[Ed]

Hi,
I've tried generating fcs files based on the above. I didn't want to use the java as I wanted a dialogue that allowed users to select the parameters to convert.
I'm not having any luck loading my files or the sample file into flowjo though on windows v.7.6.1. I just get an invalid FCS message when I drag and drop into FlowJo.
I've checked my delimiters and the data looks ok (ASCII 13 as a carriage return, AscII 9 as a tab). Any ideas?

[maciej simm]

Ed, the "roll your own" post refers to a way of doing this specifically with the Macintosh versions of the software. I've since created a java utility with a graphical user interface that will take CSV files and write FCS files. Let me know if you want to try that. simm at treestar dot com.