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https://github.com/akikuno/ctrl-mutagenesis

Code Repository used in Morimoto et al (2024)

https://github.com/akikuno/ctrl-mutagenesis

Science Score: 13.0%

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    Low similarity (6.9%) to scientific vocabulary
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Repository

Code Repository used in Morimoto et al (2024)

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  • Stars: 1
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
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Created over 4 years ago · Last pushed over 1 year ago
Metadata Files
Readme License

README.md

CTRL-Mutagenesis

  • The code quantifies the amount of sgRNA cassettes in FASTQ reads.

Requirements

  • bash
  • R (>4.0)
    • tidyverse

Procedure

  • Prepare a directory including FASTQ files

  • Save the gRNA sequence information in CSV format with the first column as ID and the second column as sequences

    • Refer to data/grna.csv.

  • Based on the PATH of the FASTQ directory and the gRNA sequence table, run the following command:

bash bash scripts/00-format.sh <PATH of the FASTQ directory> <PATH of gRNA sequence table> Rscript --vanilla --slave scripts/01-visualize.R -w=15 -h=50 -ncol=4

  • In Rscript, you can specify the width, height and number of colmuns of the plot using the -w, -h and -ncol options, respectively.
    • The default values are -w=15, -h=50 and ncol=4.

Output

  • Results are outputted in the folder reports/{analysis date}.
    • Refer to reports/2022-05-30

Owner

  • Name: Akihiro Kuno
  • Login: akikuno
  • Kind: user
  • Location: Tsukuba, Ibaraki, Japan
  • Company: University of Tsukuba

Bioinformatician working at the Laboratory Animal Resource Center

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