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boutroslab / cld_docker

Docker for CRISPR Library Designer | https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0915-2
GNU General Public License v2.0
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question about purpose and scores #2

Open huqingtao2018 opened 5 years ago

huqingtao2018 commented 5 years ago

Hi, there,

I have serveral questions. Would you please help me about them ?

I set the purpose=CRISPRa and purpose_exclusive=1, and I read the final report that some gRNA were excluded because they were not amenable for CRISPRa. Which score does it use and what is the cutoff to excluded gRNAs ?

Which kind of Doech Score and Xu Score does CLD use by default, knockout model or activation/repression model? Or CLD will swith according to the purpose parameter?

can I run CLD using multi-cpu to make it faster? Now I'm running it on linux CenOS system.

Thany you. Best wishes. Qingtao Hu

fheigwer commented 5 years ago

Hi, The sgRNA exclusion because of "not amenable for CRISPRa" is triggered when an sgRNA targets outside the specified region around the TSS (transcription start site). So its a rather hardcoded cutoff that depends on the genomic region rather than a quantitative score. By default, CLD will calculate the Doench and Xu score but use neither of them for ranking them. CLD, by default, uses the GC content and sequence variance determined E-Score to rank binding efficacy of sgRNAs. CLD should automatically detect the number of cores your computer has and scale accordingly. If you run the dockerized version, make sure you assign more cores to the docker engine (see the command adaption here: https://stackoverflow.com/questions/37871540/how-many-cpus-does-a-docker-container-use).