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liumz93 / PEM-Q

a pipeline to process data of PEM-seq or data similar, which is more comprehensive than superQ
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Off-target hotspot identification #3

Open Anna-xu408 opened 1 year ago

Anna-xu408 commented 1 year ago

Hi, if i want to call offtarget hotspots, which file as input/ Thank you!

liumz93 commented 1 year ago

Hi Anna, you can convert the final translocation tab file into bed file, and use the bed file to call peak. Thanks!

bnjvrjnke commented 1 year ago

Hi, Thanks for your great jobs. I want to reproduce the 9 off-target results of SpCas9-MYC1-CC059a in https://doi.org/10.1016/j.xpro.2021.101088. I would like to know what is the threshold of off-target site filter? I found "Off-target sites were defined as hotspots that contained genomic sequence differing from the on-target sequence by less than or equal to one-half the targeted sequence length." from https://doi.org/10.1038/nbt.3101. Does this mean that the mismatch with SpCas9 sgRNA is less than or equal to 11? Is bulge allowed? Thanks again.