Getting the coordinates of targeted locations by sgRNAs

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4.3 years ago

Sara ▴ 240

I have performed CRISPR-CAS9 exprimrnt which was followed by WGS. now I am trying to find the locations that are targeted by the sgRNAs. do you the steps that I should follow or the tools that I can use? so far I aligned the reads to the reference genome and have the bam files.

next-gen • 598 views

ADD COMMENT • link 4.3 years ago by Sara ▴ 240

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Some more details are necessary. Is this a knockout attempt with two gRNAs flanking a certain region or was a new piece of DNA introduced or was introduction of SNPs the goal? Essentially, what is the trace your Cas9 is supposed to leave in the genome?

ADD REPLY • link 4.3 years ago by ATpoint 82k

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@ATpoint: basically we have used this technique to find the structural variants at the off-target sites.

ADD REPLY • link 4.3 years ago by Sara ▴ 240

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So not really related to CRISPR but rather normal WGS and SV scanning. Then it comes down to using any structural variant caller to find SVs. Prominent choices could be Lumpy, Manta, Pindel and many more. Please browse this forum and the web for tools and benchmarks.

ADD REPLY • link 4.3 years ago by ATpoint 82k

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