Dear #C03PADVJ8RL users, I was wondering if nf-core/crisprseq can run the "targeted" analyses with many e.g., n=50 targets. With the provided example samplesheet, it seems that we can run for 1 target/protospacer and many samples. My use-case is kind of the opposite: i.e., one/few samples but many targets. Thanks for the help 😉

hi @Ashot Margaryan, do you need the results for all the targets aggregated in one output?

Thanks for the prompt feedback @Júlia Mir 🙂. Yeah, I was thinking in one, but different files may also work. In that case I guess I will have to treat each row as "different" samples? I.e., give different sample name for each row, even though they are the same (same fastq files), or would giving them the same name would work? Also, it seems like with the repeated version, the same fastq files need to be mapped e.g., 50 times, while in theory they could only be mapped once (to all target regions at once) and then extracted for downstream processes, that will probably be more efficient, but not sure 😉.

you will have give a different sample name and treat them as different samples for this to work

Hi @Júlia Mir, sorry for the long silence, I was away. Thanks for the details, I've now created a feature request: https://github.com/nf-core/crisprseq/issues/245