Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2017 May 15;18:379. doi: 10.1186/s12864-017-3746-y

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© The Author(s). 2017

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

PMC Copyright notice

Fig. 3 — Unique read aggregation into peaks for the identification of potential nuclease cleavage sites. Strand-specific unique reads defined by the GUIDE-seq dsODN integration site and the read 2 genomic reference sequence strand are aggregated over a user-defined window size (20 base default) to define strand-specific peaks. Windows with a read number greater or equal to a user-defined threshold (default = 5) are called peaks. In addition, the signal to noise ratio (SNratio) and a p-value are computed based on the local background window size (defaults 5 kb and Poisson distribution), which can also be employed as filters if desired. For each integration site, the Crick peak should precede the corresponding Watson peak based on the library construction method [19]. Consequently, this order is required to combine counts from the Watson and Crick peaks over a user-defined window size (40 base default). This aggregate “score” is used to rank peaks. The genomic region surrounding each peak (adjustable variables, default 20 bases on each side) is used to search for sequences with homology to the nuclease sequence preference (based on the input guide sequence (gRNA.file) and the PAM sequence (PAM), and the allowed mismatches within each element defined by the parameters: max.mismatch, PAM.pattern and allowed.mismatch.PAM. The GUIDE-seq data shown were generated in house for SpCas9 programmed with a sgRNA to recognize VEGFA site 2 (TS2; protospacer underlined, PAM in red) [11], where the most common dsODN integration site falls at the expected cleavage site within this sequence (green line, hg19)