Hi, and thank you for developing this great tool!
I’m trying to run CRISPresso2‑WGS on ONT and PacBio HiFi WGS data. My BAMs contain raw minimap2 alignments (no filtering) and when ran, most jobs fail to produce output (e.g. no ""). However, it works smoothly when I remove secondary alignments from ONT bams.
Therefore, I wanted to kindly ask:
1. Can CRISPresso2‑WGS be used reliably with raw (i.e. no filtered) ONT or HiFi BAM files? Would this be even recommended? The reason why I want raw, is because I am interested in highly repetitive loci and would like to keep the secondary and/or supplementary (for now)
2. If so, do you have any suggestions on how it could work with long reads?
3. I am aware that there is CRISPRlungo, which is designed for long‑read amplicons, but my data is unfortunately not amplicon‑based.
Thank you very much for your patience and any guidance and feedback.
Best,
Hi, and thank you for developing this great tool!
I’m trying to run CRISPresso2‑WGS on ONT and PacBio HiFi WGS data. My BAMs contain raw minimap2 alignments (no filtering) and when ran, most jobs fail to produce output (e.g. no ""). However, it works smoothly when I remove secondary alignments from ONT bams.
Therefore, I wanted to kindly ask:
1. Can CRISPresso2‑WGS be used reliably with raw (i.e. no filtered) ONT or HiFi BAM files? Would this be even recommended? The reason why I want raw, is because I am interested in highly repetitive loci and would like to keep the secondary and/or supplementary (for now)
2. If so, do you have any suggestions on how it could work with long reads?
3. I am aware that there is CRISPRlungo, which is designed for long‑read amplicons, but my data is unfortunately not amplicon‑based.
Thank you very much for your patience and any guidance and feedback.
Best,