The mouse clicking interface of GenomeStudio is so unfriendly for large and continuous data production. - Do we have alternatives to this that can process Illumina genotyping array idat files? - Or do you have any suggestions to automate the GenomeStudio process with command lines? Thanks
The crlmm package in R should be able to do it. However, in my own experience it is difficult to run it for Omni5 generated data. I guess it depends on which genotype array you are using. Alternatively, beadarray should also be able to read idat files but I have not tried that package yet.
You can use Illumina proprietary GenCall algorithm to generate GTC files out of IDAT file, there are now two approaches:
(i) using the Illumina Array Analysis Platform
(ii) using the Illumina Beeline/AutoConvert software
I describe how to use either approach on Linux here
Hey, is this still the "official" approach if not wanting to use GenomeStudio?
as mentioned above, some basic functions can be done in command line in windows.
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I am basically in the same spot. I just started looking at genomestudio today, so I have not dug very deep yet. I'm sure they worked really hard on this, but a windows only GUI bioinformatics tool is a bit odd. Did you end up coming across any alternatives?
It seems some basics can be done with GS command lines, but still in windows.
Did you do this? I poked around genomestudio. I see an option to use c# scripts but can find no information at all about using this functionality through googling. I want to do some manipulations to the full data table before exporting, but for the life of me can't find a way to do that within gneomestudio.
Hey, did you find a good solution? I've just been tasked with GenomeStudio...