Detailed steps for testing with real data

SRP198941_SLX15021_GEP00005 steps

If you only wish to run a demo instead of a full analysis, use these detailed steps for testing with real data subset.

Running the full analysis below will take more than four hours on a laptop.

Start GenEditID WebApp, and setup a project for analysing SRP198941_SLX15021_GEP00005

Create a project, upload the submission spreadsheet associated with this project from data/submission_spreadsheets/SRP198941_SLX15021_GEP00005.xlsx into the WebApp.

Start GenEditID WebApp

conda activate geneditid
cd ~/GenEditID/
./scripts/start_webapp.sh

Go to http://localhost:8080
Create a new project, note the GEPID
Upload the submission spreadsheet associated to this project

The active environment, the one you are currently using, is shown in parentheses () or brackets [] at the beginning of your command prompt.

(geneditid) $

if not, activate it using conda activate geneditid before running the next steps.

Download and prepare fastq files

While waiting for the submission spreadsheet to load, open a new terminal and download the public fastq files. Don’t forget to activate conda’s environment using conda activate geneditid before merging the reads.

cd ~/GenEditID/
./scripts/get_data_SRP198941_SLX15021_GEP00005.sh

All the fastq files related to this project will be stored in the PROJECTS/SRP198941 folder. Combine paired-end reads by merging reads to generate .fqjoin.gz files for amplicount analysis (seqkit needs to be installed).

cd PROJECTS/SRP198941_GEP00005
../../scripts/run_mergereads.sh

Move the joined fastq files into the PROJECTS/GEPID/fastq/ replacing GEPID with the identifier of this project.

mv *.fqjoin.gz ../GEPID/fastq/.

Run `amplicount` analysis

cd ~/GenEditID
source venv/bin/activate
cd PROJECTS/GEPID
geneditid_run_amplicount

Replace GEPID with the identifier of this project.

Visualise results

View the output of the analysis in the output result file GenEditID/PROJECTS/GEPID/amplicount.csv
Restart GenEditID WebApp: first stop the WebApp started previously by typing Ctrl-C in the terminal where it was ran, and re-run
```
./scripts/start_webapp.sh
```
Generate and visualise plots in the GenEditID WebApp http://localhost:8080. Click on the ‘GEPID’ of the project in the table of projects on the home page and navigate to the Reads, Variants and Scores tabs. After loading the spreadsheet, you need to return to the home page and click on the ‘GEPID’ of the project to generate the plots. Plot and results files are generated and stored in the project folder for convenience:
- Read coverage: GenEditID/PROJECTS/GEPID/geneditid_plots/coverage.html
- Variants impact frequency: GenEditID/PROJECTS/GEPID/geneditid_plots/impacts.html
- Scores on plate: GenEditID/PROJECTS/GEPID/geneditid_plots/koscores.html
- Targeted search: GenEditID/PROJECTS/GEPID/geneditid_plots/targeted_search.html

Two other real data projects to analyse if you wish

To analyse project SRP199742_SLX15026_GEP00009, use this submission spreadsheet data/submission_spreadsheets/SRP199742_SLX15026_GEP00009.xlsx, download the fastq files using ./scripts/get_data_SRP199742_SLX15026_GEP00009.sh and go to the cd PROJECTS/SRP199742_GEP00009 project to combine paired-end reads.
To analyse project SRP199742_SLX15025_GEP00010, use this submission spreadsheet data/submission_spreadsheets/SRP199742_SLX15025_GEP00010.xlsx, download the fastq files using ./scripts/get_data_SRP199742_SLX15025_GEP00010.sh and go to the cd PROJECTS/SRP199742_GEP000010 project to combine paired-end reads.

Back to the main manual

GenEditID Manual: detailed steps