| Input file |
i |
Mandatory |
Path to input BED file. |
| Genome |
g |
Mandatory |
Path to genome in FASTA format. |
| Off Targets |
t |
1,0,0,x,x |
String with maximum number of off-targets allowed with 0,1,2,3 and 4 mismatches (x: no limit). |
| Output prefix |
o |
“sgRNA_pairs” |
Path/prefix of output files. |
| Number of sgRNA pairs per target |
n |
10 |
Maximum number of pairs to be returned. |
| Upstream design region (bp) |
du |
500 bp |
Length of upstream region for protospacer search. |
| Downstream design region (bp) |
dd |
500 bp |
Length of downstream region for protospacer search. |
| Upstream exclude region (bp) |
eu |
100 bp |
Length of upstream region adjacent to target excluded from protospacer search. |
| Downstream exclude region (bp) |
ed |
100 bp |
Length of downstream region adjacent to target excluded from protospacer search. |
| Diversity |
v |
0.5 |
The maximum fraction of returned pairs that contain the same protospacer. |
| Individual score |
si |
0.2 |
The minimum score individual protospacers must have to be considered. |
| Paired score |
sp |
0.4 |
The minimum combined score that a protospacer pair must have to be considered. |
| Score combination |
sc |
sum |
Method by which individual scores are combined to yield pair score: addition (“sum”) or multiplied (“product”). |
| Ranking method |
r |
score |
Criteria for ranking protospacer pairs (“score” or “distance”). |
| Construct method |
c |
none |
Method applied when making protospacer pairs and oligo construction: “none” or “DECKO” (first protospacer starts with G) |
| Positive mask |
mp |
- |
Favoured regions from genome, in BED format. |
| Negative mask |
mn |
- |
Disfavoured regions from Genome, in BED format. |
