User: XIN1988

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XIN19880
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Posts by XIN1988

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Comment: C: Question: Easy way to fetch the first exons from genome
... Hi Hervé, I am trying to design the genome-wide gRNA libraries for several different species. One paper described a pipeline for the design. Basically, they first select the exonic guide sites fitting the pattern G(N16–19)NGG, and then annotate these guide sites as targeting Ensembl GRCh37 genes mod ...
written 24 days ago by XIN19880
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Comment: C: Question: Easy way to fetch the first exons from genome
... Thank you very much, Hervé. Really helpful! ...
written 24 days ago by XIN19880
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CRISPRseek gRNA searching
... Hi Julie, I have read a paper titled "Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens",and have found one approach described is interesting for design the sgRNA. Basically, they first select the exonic guide sites fitting the pattern G(N16–19)NGG, and ...
annotation written 24 days ago by XIN19880 • updated 24 days ago by Julie Zhu4.1k
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pipeline for gRNA libraries design
... Hi everyone, I am trying to design the genome-wide gRNA libraries for pig. Would anyone know any pipeline that I can adopt for this purpose? ...
annotation written 29 days ago by XIN19880
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Comment: C: Question: Easy way to fetch the first exons from genome
... Hi Hervé, Thank you very much. Sorry for the unclear description. Actually, I want to retrieve the first exons for each gene where RNA polymerase begins transcribing. The reason that I will use the retrieved exon for CRISPR gRNA design as targeting on these regions would give high efficient knocko ...
written 29 days ago by XIN19880
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Question: Easy way to fetch the first exons from genome
... Hi I am wondering which way could allow me to retrieve the first exons from genome with the information of the exon length. the purpose is to retrieve the first exons for gRNA design. Thanks, Xin ...
annotation written 4 weeks ago by XIN19880 • updated 29 days ago by Hervé Pagès ♦♦ 14k
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Comment: C: CRISPR SEEK TxDb issue
... Hi Julie, Thank you very much for your quick response. The problem has been resolved by following the script from James and Hervé. I will try several sequences following the vignettes for the design. Thanks again, Xin ...
written 4 weeks ago by XIN19880
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Comment: C: CRISPR SEEK TxDb issue
... Thank you very much, James! ...
written 4 weeks ago by XIN19880
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CRISPR SEEK TxDb issue
... Hi everyone, I tried to use CRISPR seek to design gRNA for pig gene. Below error occurred. However, there are no txdb for pig genome existing. How to figure it out? ``` Error in offTargetAnalysis(inputFilePath2, findgRNAsWithREcutOnly = FALSE, : To indicate whether an offtarget is inside an e ...
annotation written 4 weeks ago by XIN19880 • updated 4 weeks ago by Julie Zhu4.1k

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