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usage:batch_processing [2019/12/20 18:36] – pseudomoaner | usage:batch_processing [2020/06/26 11:48] (current) – [Installing Double FAST] pseudomoaner | ||
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The .m files required to run Double FAST are included in the main distribution of FAST, available from the [[setup: | The .m files required to run Double FAST are included in the main distribution of FAST, available from the [[setup: | ||
- | Double | + | To run, double |
- | ===== Editing the Double FAST script ===== | + | ===== Using Double FAST script ===== |
To run Double FAST, you will need to perform two tasks: | To run Double FAST, you will need to perform two tasks: | ||
- Run FAST once on a single dataset, using the standard GUI. This generates files containing the settings used for each stage of the analysis. | - Run FAST once on a single dataset, using the standard GUI. This generates files containing the settings used for each stage of the analysis. | ||
- | - Directly edit the DoubleFAST.m script. | + | - Set up the DoubleFAST.m script. |
- | If you are not used to editing code directly, don't panic! All you need to do is tell the software where your datasets are, and what stages in the analysis you would like to perform. By leaving these stages in your hands, | + | If you are not used to editing code directly, don't panic! All you need to do is tell the software where your datasets are, and what stages in the analysis you would like to perform. By leaving these stages in your hands, |
Once you have run FAST on your initial dataset, open the DoubleFAST.m script, available within the DoubleFast directory of your FAST installation. At the top of this script are the key variables that you need to define. | Once you have run FAST on your initial dataset, open the DoubleFAST.m script, available within the DoubleFast directory of your FAST installation. At the top of this script are the key variables that you need to define. | ||
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By default, this is set up assuming a root-branch structure as shown below: | By default, this is set up assuming a root-branch structure as shown below: | ||
- | < | + | {{ :usage:batchprocessfiles.png? |
- | | RRR | | | | | | | | | |RRR{background-color:# | + | |
- | | |!| | | | | | | | | | | + | |
- | | |)|-|-| EE1 | | | | |EE1{background-color:# | + | |
- | | |!| | | |!| | | | | | | + | |
- | | |!| | | |`|-|-| IM1 |IM1{background-color:# | + | |
- | | |!| | | | | | | | | | | + | |
- | | |)|-|-| EE2 | | | | | |EE2{background-color:# | + | |
- | | |!| | | | | | | | | | | + | |
- | | |`|-|-| EE3 | | | | | |EE3{background-color:# | + | |
- | </ | + | |
However, this can be flexibly adjusted according to your requirements. The only requirement is that **batchRoots** is defined as a cell array containing the paths to all of your datasets. | However, this can be flexibly adjusted according to your requirements. The only requirement is that **batchRoots** is defined as a cell array containing the paths to all of your datasets. | ||
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</ | </ | ||
- | Note that all of your raw files should have the same name, with their identity specified by their position in the file structure. For example, to process replicate 1 of experimental condition 2, you would give the corresponding raw dataset the filename ' | + | Note that all of your raw files should have the same name, with their identity specified by their position in the file structure. For example, to process replicate 1 of experimental condition 2, you would give the corresponding raw dataset the filename ' |
Finally, you tell Double FAST where it can find the settings files defined during the initial run through FAST: | Finally, you tell Double FAST where it can find the settings files defined during the initial run through FAST: | ||
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</ | </ | ||
- | Once you have finished setting up Double FAST, you can run it simply by pressing the ' | + | Once you have finished setting up Double FAST, you can run it simply by pressing the ' |
- | ===== Video demonstration ===== | + |