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)
Method¶
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.