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We use STAR Solo to map results of CRISPR screens, specifically at one of the steps we map guide RNA reads that we have introduced and assign them to cells . For that we generate artificial reference,…
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I am writing to you because I am collaborating in a CRISPR/Cas9 knockout screening analysis. We are using the GeCKO v2 gRNA library and we found that a huge number of gene symbols are outdated. I foun…
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python /seqprg/scripts/gene_editing/primedesign.py -f design.txt -pbs 10 11 12 13 14 15 -rtt 10 11 12 -nick_dist_max 10
2022-07-28 21:00:47,188 - INFO - Searching for pegRNAs and nicking gRNAs for …
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I am sorry that I am a beginner for perturb-seq, I want to know how I can use the result of sceptre for the input of seurat? Can the sceptre do clustering?
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I was having trouble running the script: `CRISPR/download_data.sh`. In debugging, it turns out that the tables are no longer hosted at the URI in the script.
See: [https://images.nature.com/origin…
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The regular read_10x_h5() function neglects the gRNA in scRNA-seq CRISPR data which were provided to cell ranger (does not show In adata.X and adata.var). However, with the read_mtx() it is included i…
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Should be possible to add several guide RNAs and a single repair DNA (if any)
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dear sir,
Can SPROUT output the insertion/deletion position on the target sequence?
Just like FORECasT and inDelphi.
best
likuan
PEHGP updated
3 years ago
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I guess with 5'/3' PAM setting, the position/direction on the cDNA and genome is kind of reversed in the case of transcripts in reverse strand. Might be worth it to just get rid of the 5'/3' setting a…
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TypeError: undefined is not an object (evaluating 'interaction.participants[i].segment.role = null')
[yeast_gates_network_example.zip](https://github.com/VisBOL/visbol-js/files/2550499/yeast_gates_…