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Topic: MS-DIAL Linux console parameter file (Read 318 times) previous topic - next topic

MS-DIAL Linux console parameter file

Hi MS-DIAL developers,

Thanks for making such a good software! I am using Linux console app (v4.80) and have several questions regarding the parameter file.
  • How to specify the target omics (metabolomics/lipidomics) in the parameter file? In the “start up a project” tab (see pic), I can select either metabolomics or lipidomics.
  • How to specify "reference file (see pic)" in the parameter file? According to the source code in ConfigParser.cs, I assume it is “Alignment reference file ID”. However, since it only take integer instead of string as variable, how do I get the ID corresponding to each sample?
  • How to specify the number of threads in the parameter file? Or does it automatically use all the available threads?

I'd really appreciate your help and look forward to hearing from you.

Best,
JC

Re: MS-DIAL Linux console parameter file

Reply #1
Hello,

We have a similar issue with the Windows console app regarding question no. 2. We often have a blank at the beginning of the injection sequence and if a blank is chosen automatically as the reference file for peak alignment, will it cause a major issue for this process since it probably doesn't contain peaks from most metabolites?

Best regards,
Ville