COVID qPCR Analyzer can be executed with GUI:
Execution in Linux
$ unzip COVIDqPCRAnalyzer.zip
$ cd COVIDqPCRAnalyzer
$ Rscript /home/user/COVIDqPCRAnalyzer.R
Execution in Windows
1. Extract COVIDqPCRAnalyzer.zip
2. open CMD
3. Enter:
"<PATH to Rscript program>" "<Path to R file COVIDqPCRAnalyzer.R>"
e.g.
"C:\Program Files\R\R-*.*.*\bin\Rscript.exe" "C:\Users\Desktop\COVIDqPCRAnalyzer.R"
COVID qPCR analyser provides the function to select the various variables of qRT-PCR result file. Following are the entries that are required to be filled before proceeding the run:
1. Input file (.xls)
Select the real time PCR result file (containing Ct values for tested samples) in this field. The file format accepted by the tool is excel (.xls).
2. Exp ID
This field requires the unique run ID/name of the experiment that user will be using in the analysis.
3. Date
Date of experiment run is required to be filled in this field.
4. Data start row (excl. info headers)
Fill the field with number of row from where the actual Ct value data starts in the qPCR result file. Fill the row number after excluding the header rows which usually contain the information of real time PCR machine and other technical details.
5. Ct Column ID (e.g. A,B,C,D...)
Fill the field with the column ID (e.g. A or B or C or D) which contains the Ct values of target and control genes.
6. Ct cutoff value
Fill the field with the cutoff Ct value of real time PCR result. This threshold value is required by the tool for analysing the results -“positive”, “negative” or “invalid”.
7. Gene ID column
Fill the field with the ID of the column (e.g. A or C or H) with Target gene and control gene ID information in real time PCR raw data file.
8. Sample ID column
Fill the field with the ID of the column (e.g. A or C or H) with Patient sample ID information in real time PCR raw data file.
9. Well ID column
Fill the field with the ID of column (e.g. A or C or H) with Well position information in real time PCR raw data file.
10. Output filename
Choose the destination folder location and output filename.
11. NTC well ID (e.g. A23 or G15)
Fill the field with the Well ID (with column ID and row number, for ex: A23 or G15) of the real time PCR plate, in which reaction with no template control is loaded.
12. Positive control sample well ID
Fill the field with the Well ID (with column ID and row number, for e.g.: A23 or G15) of the real time PCR plate, in which reaction with Positive control sample is loaded.
13. Negative control sample well ID
Fill the field with the Well ID (with column ID and row number, for e.g.: A23 or G15) of the real time PCR plate, in which reaction with Negative control sample is loaded.
Once all the informations are filled in GUI, proceed with the run by clicking at “Submit” button. As soon as the user starts the run, tool will generate the output file which contain the results of SARS-CoV-2 infection presence/absence. The run time for COVID qPCR would be fractions of seconds. Thereby, make this quick tool for real time PCR data analysis.
COVID qPCR Analyzer report:
The output report file will be a .CSV file and contain five columns with the following information:
1. Sample ID name
This column will have all the samples names which has been analysed by COVID qPCR analyzer using GUI.
2. Well ID column
This column contains the information of wells ID tested for the analysis.
3. Exp. ID
This column will have the same experiment ID that was given by user while submitting the details in GUI.
4. Test result
This column will contain the results generated by COVID qPCR analyzer. For example-based on specified Ct value the samples would be called “positive”, “negative” and “invalid” for SARS-CoV-2 infection.
5. Date
This column will give the date on which the experiment run was conducted.