Crispresso2 for Prime Editor¶
usage: crispresso2_PE.py [-h] [-j JID] [-s SCAFFOLD_SEQUENCE] -f PE_INPUT
[-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:
crispresso2_PE_yli11_2020-09-05)
-s SCAFFOLD_SEQUENCE, --scaffold_sequence SCAFFOLD_SEQUENCE
-f PE_INPUT, --PE_input PE_INPUT
input list (default: None)
Genome Info:
-g GENOME, --genome GENOME
genome version: hg19, hg38, mm9, mm10. By default,
specifying a genome version will automatically update
index file, black list, chrom size and
effectiveGenomeSize, unless a user explicitly sets
those options. (default: hg19)
--genome_fasta GENOME_FASTA
genome fasta file (default:
/home/yli11/Data/Human/hg19/fasta/hg19.fa)
Summary¶
Running crispresso2 for prime editor mode: https://github.com/pinellolab/CRISPResso2
The command is:
CRISPResso -r1 ${COL1} -r2 ${COL2}
--amplicon_seq $amplicon
--prime_editing_pegRNA_spacer_seq ${COL6}
--prime_editing_pegRNA_extension_seq ${COL7}
--prime_editing_nicking_guide_seq ${COL8}
--prime_editing_pegRNA_scaffold_seq {{scaffold_sequence}}
--write_cleaned_report
-o {{jid}}/${COL3}
Input¶
A 8-column tsv file.
Read1 Read2 Output_Name Forward primer Reverse primer pegRNA spacer sequence pegRNA extesion sequence ngRNA sequence
Usage¶
hpcf_interactive
module load python/2.7.13
crispresso2_PE.py -f input.list
Output¶
Once the job is finished, you will receive a notification email.
Comments¶
code @ github.