Before attempting #14 to convert idat to gtc in unix we should make sure it works in Windows, as designed. In truth, Illumina doesn't support running this on the command line, though I'm told it should work. I tried running on a windows command line and couldn't get it working. It started to run and then gave an error in a popup window and froze.
beeline is the GUI used to run AutoConvert.exe. I'm not sure if the version that comes with beeline is different than the stand alone version that you can download. We may gain some insight by running beeline as well. When you run through beeline a command prompt opens up and you can see some output.
Before attempting #14 to convert idat to gtc in unix we should make sure it works in Windows, as designed. In truth, Illumina doesn't support running this on the command line, though I'm told it should work. I tried running on a windows command line and couldn't get it working. It started to run and then gave an error in a popup window and froze.
Here's what needs to be done:
Download AutoConvert: https://support.illumina.com/array/array_software/beeline/downloads.html Run like this:
AutoConvert.exe /path/to/IDAT/dir /path/to/output/directory /path/tomanifest.bpm /path/to/cluster_file.egt
beeline is the GUI used to run AutoConvert.exe. I'm not sure if the version that comes with beeline is different than the stand alone version that you can download. We may gain some insight by running beeline as well. When you run through beeline a command prompt opens up and you can see some output.