DVsc User Manuals

Web version

Click on the "analysis" module in the navigation bar at the top of the homepage.

Drag the original fastq files to the upload box, or click on the upload box to upload the files.

After all files are uploaded successfully, click the "Run" button.

Please fill in the configuration information. If it is bulk RNAseq, keep the default settings. If it is single-cell data, select "single-cell RNA-seq" for "Seqtype", and choose the corresponding barcode length and UMI length in the "barcodenum" and "uminum" columns according to the experimental design. For example, for the demo, select 16 and 12, respectively. Then, click the button.

Later, the page will be redirected to the following page. At this time, the background is analyzing the data. Please do not close the page during the analysis. You can refresh the page at any time. When the task is completed, the result file will be automatically downloaded to the local computer after refreshing the page.

Local version

1. Download profile[Link] and source code[Link] of DVsc. One should also download the human reference[Link], virus reference[Link] and virus annotationVirus annotation databases[Link] databases.

2. Set up the conda environment. Note that ${download_dir} is the path you download the files.

		
		conda create --name DVsc --file ${download_dir}/environment.txt
		conda activate DVsc
		
		

3. Run Here we take the demo data as examples. the demo data can be download from http://62.234.32.33:5000/download.

• Single-cell RNAseq

		
	  python analysis.py --input demosc_1.fastq,demosc_2.fastq  --sample demosc --seqmethod scRNAseq \
	  --outpath ./demosc --barcodenum 16 --uminum 10 --humdb ${download_dir}/homoDB/homo --virdb ${download_dir}/virusDB/virus \
	  --annotatefile ${download_dir}/virusanno.txt
      
		

• Bulk RNAseq

		
	  python analysis.py --input demobulk.fastq  --sample demosc --seqmethod bulkRNAseq \
	  --outpath ./demosc --barcodenum 16 --uminum 10 --humdb ${download_dir}/homoDB/homo --virdb ${download_dir}/virusDB/virus \
	  --annotatefile ${download_dir}/virusanno.txt
      
		

Explanations of the output files

Single-cell RNAseq

The results include two files: "viruscount.filter.txt" and "umi.filter.txt".

In the "viruscount.filter" file, you will find the basic information about the detected viruses. The first column represents the sample names, the second column represents the virus names, the third column represents the count of virus, and the fourth column represents the abundance of each virus.

In the "umi.filter.txt" file, you will find the UMI (Unique Molecular Identifier) information for the detected viruses. The first column represents the virus names, the second column represents the UMI sequences associated with each virus, and the third column represents the count of virus.

Bulk RNAseq

The results include one file: "viruscount.filter.txt". The first column represents the sample names, the second column represents the virus names, the third column represents the count of virus, and the fourth column represents the abundance of each virus.