FAQs:

1. What is VISPR-online?

VISPR-online is a web-based interactive framework for CRISPR screens exploration and visualization. CRISPR screening helps systematically exploration of the functions of coding and non-coding elements in a genome. We previously developed VISPR, bundled with MAGeCK, an interactive framework to visualize CRISPR screening results in a local computer. However, VISPR only supports output of MAGeCK, and requires manual installation and configuration. To overcome these limitations, we developed VISPR-online, a web-based server for the visualization of CRISPR screening.
The advantages of VISPR-online compared with VISPR:

  • Interactive gene essentiality exploration.
  • Support more popular CRISPR screening analysis tools, including MAGeCK, BAGEL, and JACKS.
  • View gRNAs in their genomic context.
  • Provide retrieving and sharing session functions.
  • Installation and configuration free.

2. How to obtain the input files of VISPR-online?

VISPR-online is a downstream tool for MAGeCK, BAGEL and JACKS. The input of VISPR-online is output of these tools. For the usage of these tools, please refer to related papers. Besides, we provide a test dataset for these three tools, and the download link is on the main page of VISPR-online.

3. Format of sgRNA location file.

sgRNA location file is a tab-delimited text file without file header. Five columns are required: chromosome name, gRNA start, gRNA stop, gRNA ID and strand. The gRNA IDs should be the same with those in read count file.

chr2	11143961	11143981	s_7648	-
chr3	186801168	186801188	s_46884	+
chr20	46053591	46053611	s_50992	+
chr3	46705812	46705832	s_57876	+
chr19	46634669	46634689	s_23309	-
chr7	108514201	108514221	s_42887	+

4. How to resume session and share data?

VISPR-online allows users to save sessions to the server and resume them later with session IDs. If the "Save session to server" box is checked (Step 6 in "Upload Files" tab), the session will be saved to the server. VISPR-online will return a session ID to the user. Users can resume the session later with the ID ("Load Session" tab). They can also send the session ID to others to share the data.

5. Is VISPR-online open source?

VISPR-online is open source under MIT license. The source code can be downloaded from GitHub. Users can install and use VIPSR-online in a local computer or network. The README of the repository describes how to install VISPR-online locally.

6. Problem caused by browser cache.

Brower usually caches the JavaScript, CSS and other data to improve speed and user experience. When CRISP-view is updated, user needs to empty the previous cache in the browser. For Safari, press Opt+Cmd+E to empty cache.