> For the complete documentation index, see [llms.txt](https://molgenis.gitbook.io/molgenis-pipelines/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://molgenis.gitbook.io/molgenis-pipelines/ngs_rna/rna-run.md).

# Run

## 1) Copy rawdata to rawdata ngs folder

```bash
scp –r SEQSTARTDATE_SEQ_RUNTEST_FLOWCELLXX username@yourcluster:${root}/groups/$groupname/${tmpDir}/rawdata/ngs/
```

## 2) Create a folder in the generatedscripts folder

```bash
mkdir ${root}/groups/$groupname/${tmpDir}/generatedscripts/TestRun
```

## 3) Copy samplesheet to generatedscripts folder

```bash
scp –r TestRun.csv username@yourcluster:/groups/$groupname/${tmpDir}/generatedscripts/
```

***Note: the name of the folder should be the same as samplesheet (.csv) file***

## 4) Run the generate script

```bash
module load NGS_RNA
cd ${root}/groups/$groupname/${tmpDir}/generatedscripts/TestRun
cp $EBROOTNGS_RNA/generate_template.sh .
sh generate_template.sh
cd scripts
```

***Note:*** if you want to run locally, you should change in the CreateInhouseProjects.sh script the backend (this can be done almost at the end of the script where you have something like: sh ${EBROOTMOLGENISMINCOMPUTE}/molgenis\_compute.sh search for –b slurm and change it into –b localhost

```bash
sh submit.sh
```

## 5) Submit jobs

navigate to jobs folder. The location of the jobs folder will be outputted at the step before this one (step 4).

```bash
sh submit.sh
```