Crispresso2 for HDR

Summary

Run CRISPRESSO HDR mode.

Input

A 6-column tsv file: R1.fastq, R2.fastq, output_name, gRNA_seq, unedited amplicon, edited amplicon

12_S12_L001_R1_001.fastq.gz     12_S12_L001_R2_001.fastq.gz     test1           cttgaccaatagccttgaca            Amplicon_seq1           Amplicon_seq2
xxx_R1_001.fastq.gz     xxx_R2_001.fastq.gz     test1           cttgaccaatagccttgaca            Amplicon_seq1           Amplicon_seq2
../../_images/HDR_example_input.PNG

Usage

hpcf_interactive

module load python/2.7.13

run_lsf.py -f input.tsv -p crispresso_PE_HDR

## specific parameter for Azusa

run_lsf.py -f input.tsv -p crispresso_PE_HDR --HDR_parameters " --exclude_bp_from_left 1 --exclude_bp_from_right 1 --quantification_window_coordinates 20-128"

Output

Once the job is finished, you will receive a notification email.

Inside the jobID folder, you can look at the crispresso2 result. The html file is inside in each sub-folder.

Comments

code @ github.