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
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.