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Index options
Tyler Fair edited this page Oct 14, 2019
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tmpLocation- where you want to put temporary files. FlashFry will clean-up after itself, but does generate a lot of intermediate files during indexing. Its best to put this somewhere you have plenty of space. -
reference(required) - the input fasta reference file you'd like to discover off-target sequences in -
database(required) - the output database file to generate -
enzyme(optional, default to spcas9) - which enzyme to consider when making discovering sites in the reference. Options include:-
cpf1- 24 base targets with a 5' TTTN sequence -
spcas9- 23 base targets with a 3' NRG (NAG/NGG) sequence -
spcas9ngg19- 22 base targets with a 3' NGG sequence (Horlbeck et al., Elife 2016) -
spcas9ngg- 23 base targets with a 3' NGG sequence -
spcas9nag- 23 base targets with a 3' NAG sequence
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binSize(optional, default to 7) - what bin size should we use when indexing the fasta file. Originally this had a bigger effect on search speed, but now individual bins can have their own lookup tables, reducing the importance of this parameter.