Designing CAS13-gRNA

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[Input Type 1 (Ensembl IDs): example TXT] (disabled) [Input Type 2 (CSV): example CSV] [Input Type 3 (Regions): example CSV] [Input Type 4 (FASTA): example TXT] [see via GitHub]

2. Parameters
	input_type 2: CSV(ID,Seq), 3:Genomic coordinates, 4:FASTA
	n_guides Number of guides to design
	n_spacers Number of spacers within each guide
	guide_length Guide length depending on type of Cas ('23' is for Cas13)
	extension Extension of the spacers, which is useful if there is maturation (e.g. cutting) of the spacers from the Cas protein
	quality_threshold Quantile threshold (4: >75%)
	min_dist Minimum distance between each of the gRNAs that are part of the same array
	min_dist_global Minimum distance between all gRNAs that are targeting the same trasncript
	threads Number of CPU threads, change not allowed.
	min_dist_type Percentage (p) or nucleotides (n), (change not allowed)
	junction_flag Junction flag (avoid overlapping junctions). If TRUE, avoid creating guides in junction gaps (change not allowed).
	sequence_lower_range Trimming sequence (5'), change not allowed.
	sequence_upper_range Trimming sequence (3'), change not allowed.
	memory Memory size, change not allowed.
	organism human (change not allowed)
	restriction_sequences CGTCTC (change not allowed)

3.Contact information

Reference: Montero et al, Nat Methods. 2024
Source: [GitHub]
Supplementary Table3.tar.gz (%>tar xfvz tar_filename)
Supplementary Table6.tar.gz (%>tar xfvz tar_filename)

How to use
README
Expected Result (ROTFQpX1rN.tar.gz)

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