usage/reanalyzing.md

@@ -23,7 +23,7 @@ You also need to make sure you define the output directory with the `-w` argumen
 For example, if the directory structure is like:
 
 ```sh
-  📦MYPROJECT                     # main output folder
+  📦MYPROJECT                     # main output folder specified with '-w' argument
   ┣  📂NTS-XXX                    # project folder (column 4 in samplesheet)
   ┃  ┣  📂FASTQ                   # temporary folder for fastq files
   ┃  ┣  📂FASTQC                  # FastQC results
@@ -50,6 +50,19 @@ snakemake -nrp --config conf="config.json"
 ```
 If everything is fine, the pipeline **SHOULD NOT** run the `split_fastq` rule as it should find the already created `XXX.fastq.gz` in the `CUTADAPT` directory of your previously analyzed data. If this is not the case, have a look at the reasons why snakemake wants to create these files again by looking at the output of the dry run.
 
+#### Re-analyzing with sample splitting into multiple projects
+
+If you want to split the samples into multiple projects, you will have to create as many different project folders as specified in the samplesheet used.  
+Lets say half of the samples belong to project "NTS-XXX_1" and the other half to project "NTS-XXX_2". You will have to create those two folders and move the already created fastq files in the "CUTADAPT" folders in their corresponding project:
+
+```sh
+  📦MYPROJECT                     # main output folder specified with '-w' argument
+  ┣  📂NTS-XXX_1                  # project folder (column 4 in samplesheet)
+  ┃  ┣  📂CUTADAPT                # fastq files after cutadapt belonging to project 'NTS-XXX_1'
+  ┣  📂NTS-XXX_2                  # project folder (column 4 in samplesheet)
+  ┃  ┣  📂CUTADAPT                # fastq files after cutadapt belonging to project 'NTS-XXX_2'
+```
+
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