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Repository fcs_gate_trans
Synopsis: converts FCS files to text using the FCSTrans transformation, with optional automated gating.
**Input**
This tool uses FCS files as input and files are processed serially. Users choose to automatically gate cellular debris, and/or compensate the data.

**Output files**
Output is tab-separated text containing transformed fluorescence intensity values for each marker.
If the option is selected, a FCS file (format FCS3.0) is generated.
Compensation will be implemented according to the spillover matrix included in the FCS files (if available).

**Automated Gating output**
Automatically gated output includes a summary of data pre- and post-gating as well as density scatter plots pre- and post- gating for each marker pair.
Automated gating is implemented with flowDensity. Cellular debris removal uses gate coordinates calculated based on the density of the forward scatter channel only. The calculated gate is vertical and located at the largest value of either the 0.1 quantile of the FSC density or the lowest density between the first and second density peaks. Cells smaller than the threshold are removed.

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Revision: 2:66a54e77aa33
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Contents of this repository

Name Description Version Minimum Galaxy Version
with optional compensation and automated gating with flowDensity. 1.2+galaxy1 18.01

Categories
Flow Cytometry Analysis - Tools for manipulating and analyzing FCS files