Standard Operating Procedure for scripts - MeryemAk/dRNASeq GitHub Wiki

Download all requirements first!

1. start up computer in the lab an log in.

2. Open Command Prompt, type ubuntu and press enter. A welcome message will appear and the ubuntu account is activated, showing the LBR account as follows: been850@LBR

3. Clone the GitHub repository by typing:

git clone https://github.com/MeryemAk/dRNASeq.git

4. A folder names dRNASeq is automatically created. Move into this folder with:

ls           # Check whether the dRNASeq folder is created or not
cd dRNASeq   # Move into the folder

5. Make sure all scripts are executable by performing:

chmod +x *   # * selects all files

6. Activate the Conda environment by typing:

conda activate dRNAseq

When activated, (dRNAseq) should appear before the LBR account.

7. Remove the test data from the 1.data folder and move the actual data within this folder:

rm -rf 1.data/                    # Remove test data
mv /path/to/data /dRNASeq/1.data/ # Move actual data to 1.data folder

Note: this SOP continues with the test-data.

8. Navigate to the scripts folder:

cd dRNASeq/scripts

9. Run the merge script:

./2.merge.sh

A new folder called merged/ will be created under 1.data/. These contain the merged fastq files for every barcode.

10. Run QC with NanoPlot and NanoComp

./3.qc.sh

A new folder 2.qc is created, which holds both the NanoPlot reports per sample as well as the NanoComp report. The NanoPlot report is named [samplename]_NanoPlot-report.html and the NanoComp report is named NanoComp-report.html