sgRNA

A pipeline for sgRNA design

Usage

1. Rscript do_sgRNA_form_sg_noG.r foo.fa xname
2. bash do_seq2fa.sh xname
3. bash do_bt2.sh xname
4. bash do_step1.psh xname
5. bash do_step2.psh xname
6. bash do_step3.psh xname

foo.fa is the path of genomic sequence file or one chromosome in fasta format (e.g. chr9.fa).
xname is the accession name (e.g. batch1).

The output file named "xname_selected.txt" contains the sgRNA information.

Citation

Zhou, Y. et al. Painting a specific chromosome with CRISPR/Cas9 for live-cell imaging. Cell Res, doi:10.1038/cr.2017.9 (2017).