Running CRISPResso2 with more than one expected HDR template in batch mode

[sharagyaltshen]

Hello,

I'm trying to run CRISPResso on a batch of files with two potential HDR templates. I've tried entering the templates as potential amplicons but that didn't work. Would it be best to run the files with each HDR template separately? Any suggestions would be appreciated.

[kclem]

Hi @sharagyaltshen,

I'd run them with all three amplicons together (WT, HDR1, HDR2) by providing the amplicon sequences as a comma-separated list like this:

CRISPResso --amplicon_seq AAAAAAAA,TTTTTTTTT,CCCCCCCC --amplicon_name WT,HDR1,HDR2 ...

If you're running in batch mode, just provide AAAAAAAA,TTTTTTTTT,CCCCCCCC in the amplicon_seq column and WG,HDR1,HDR2 in the amplicon_name column and it should work.

If you're getting an error or it isn't working, please let me know.

[sharagyaltshen]

Hello,

Thank you for your response! I tried what you suggested, but I keep getting 0 aligned reads for one of my amplicons even though I know that I have reads that do align. This is the code I used and I've attached a few of my FASTA files if you'd like to take a look.

CRISPRessoBatch --batch_settings RNPA_B.txt --amplicon_seq GCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCG,GCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACgtTGACgTggGGCGTcCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCG,GCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACaCTcACacAtGGCGTtCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCG --amplicon_name WT,HDR1,HDR2 -g CTCGTGACCACCCTGACCTA -e GCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACgtTGACgTggGGCGTcCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCG
406_CGATGTCTTG-GAACGTTCGG_L001_R1_001.fastq.gz
406_CGATGTCTTG-GAACGTTCGG_L001_R2_001.fastq.gz
534_TGCTTCCAAG-GTAACATCTG_L001_R1_001.fastq.gz
534_TGCTTCCAAG-GTAACATCTG_L001_R2_001.fastq.gz