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jeffhussmann / knock-knock

toolkit for analyzing genome editing experiments
GNU General Public License v3.0
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Can knock-knock be used for multiplex on/off-target analysis? #1

Open gkurgan opened 4 years ago

gkurgan commented 4 years ago

Hello!

I just had a quick question. Looking through the documentation I am a little unclear if knock-knock can be used to analyze CRISPR NGS data generated using multiplexed PCR (e.g. multiple amplicon targets in a single FASTQ). This is mainly useful for simultaneous on/off-target analysis of CRISPR editing. Could you possibly provide some clarification regarding this or possibly an example of how it should be used in this case?

Thanks!

jeffhussmann commented 4 years ago

Hi Gavin -

knock-knock currently expects each FASTQ to contain a single amplicon target. To analyze the data you describe, you could preprocess your data to demultiplex each FASTQ into separate files for each target, then feed these demultiplexed files into knock-knock. I would be interested in adding built-in support for this kind of demultiplexing - if you are willing to share some example data, send me an email at jeff.hussmann@gmail.com. Thanks!