Easy-Prime: pegRNA design

usage: easy_prime.py [-h] [-j JID] -f INPUT [--PAM_seq PAM_SEQ] [-e EXTEND]
                     [-l SGRNA_LENGTH] [-o OUTPUT] [-g GENOME]
                     [--genome_fasta GENOME_FASTA]

optional arguments:
  -h, --help            show this help message and exit
  -j JID, --jid JID     enter a job ID, which is used to make a new directory.
                        Every output will be moved into this folder. (default:
                        easy_prime_yli11_2020-04-17)
  -f INPUT, --input INPUT
                        a list of variants 5 columns chr, pos, name, ref, alt
                        (default: None)
  --PAM_seq PAM_SEQ     specify the PAM sequence, e.g., NGG. (default: NGG)
  -e EXTEND, --extend EXTEND
                        Define a region to look for gRNAs, extend search area
                        to left and right (default: 200)
  -l SGRNA_LENGTH, --sgRNA_length SGRNA_LENGTH
                        sgRNA_length (default: 20)
  -o OUTPUT, --output OUTPUT
                        output file name (default: yli11_2020-04-17)

Genome Info:
  -g GENOME, --genome GENOME
                        genome version: hg19, hg38, mm9, mm10. currently, only
                        hg19 is available (default: hg19)
  --genome_fasta GENOME_FASTA
                        genome version: hs, mm (default:
                        /home/yli11/Data/Human/hg19/fasta/hg19.fa)

Summary

This tool can help you design pegRNAs given a list of variants (vcf format)

https://github.com/YichaoOU/easy_prime

Method

../../_images/easy_prime_method.gif

Input

chr11   5248232 HBB     A       T
chr15   72638920        HEXA    G       GGATA

Usage

hpcf_interactive

easy_prime.py -f input.vcf

Output

Inside the {{jobID}} folder.

Comments

code @ github.