Cas-Analyzer specifications

Information


Unique identifier OMICS_12676
Name Cas-Analyzer
Interface Web user interface
Restrictions to use None
Input data Paired-end reads, Single-end read or fastq joined file.
Input format Fastq or gzipped fastq
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Jin-Soo Kim <>

Publication for Cas-Analyzer

Cas-Analyzer in publications

 (6)
PMCID: 5899152
PMID: 29654299
DOI: 10.1038/s41467-018-03927-0

[…] sequencing using an illumina miseq instrument, according to the manufacturer’s protocol. statistical analysis and determination of modification frequency was performed using crispr-dav and cas-analyzer., single-molecule fret experiments were set up and performed using a previously described protocol. briefly, to prevent non-specific binding of samples to the glass surface, […]

PMCID: 5938013
PMID: 29622782
DOI: 10.1038/s12276-018-0037-x

[…] phusion taq polymerase (new england biolabs, ma, usa). pcr amplicons were then subjected to paired-end deep sequencing using mi-seq (illumina, ca, usa), and deep-sequencing data were analyzed using cas-analyzer (www.rgenome.net). indels 3 bp upstream of the pam sequence were considered mutations resulting from the crispr/cas9 reaction. for hdr analyses, kis were counted when specific donor […]

PMCID: 5700056
PMID: 29167440
DOI: 10.1038/s41467-017-01650-w

[…] dna polymerase (new england biolabs), and the pcr amplicons were subjected to paired-end sequencing using the illumina miseq. the pcr primer sequences are listed in supplementary table . we used cas-analyzer (http://www.rgenome.net/cas-analyzer/) to analyze the mutation frequencies., to analyze expression levels of myod and ascl1 mrna, total rna was extracted using riboclear (geneall) […]

PMCID: 5686910
PMID: 29141659
DOI: 10.1186/s13059-017-1355-3

[…] chain reaction (pcr) amplified for ngs library construction. pooled pcr amplicons were sequenced using miniseq with a truseq ht dual index system (illumina). indel frequencies were obtained using cas-analyzer []., additional file 1: figure s1. , electronic supplementary material , the online version of this article (doi:10.1186/s13059-017-1355-3) contains supplementary material, […]

PMCID: 5638908
PMID: 29026069
DOI: 10.1038/s41467-017-01051-z

[…] sequencing libraries were subjected to paired-end sequencing with the miseq system (illumina). after miseq, paired-end reads were joined by the fastq-join. fastq-joined files were analyzed using cas-analyzer (http://www.rgenome.net/cas-analyzer/) to obtain a mutation frequency in edited cells. for single-cell colony expansion, transfected cells were diluted and sorted with a density of 1 […]


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Cas-Analyzer institution(s)
Department of Chemistry, Hanyang University, Seoul, Korea; Center for Genome Engineering, Institute for Basic Science, Seoul, Korea; Department of Chemistry, Seoul National University, Seoul, Korea; Institute for Materials Design, Hanyang University, Seoul, Korea; Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
Cas-Analyzer funding source(s)
This work was supported by a grant of the Korea Healthcare technology R&D Project, Ministry for Health & Welfare Affairs (HI16C1012) and Institute for Basic Science (IBS-R021-D1).

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