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.