Options - BelenJM/supeRbaits GitHub Wiki

Quick overview and description of the options that can be used within the toolbox of supeRbaits (see Table 2 in Jimenez-Mena et al., 2021):

supeRbaits contain two functions: do_baits() and blast_baits()

do_baits()

The arguments for do_baits() are:

Argument	Description
n	Total number of desired baits
size	Length (in bp) of each bait
database	Genomic reference
n_per_seq	Number of baits per each sequence in the database (e.g. chromosome, scaffold, etc.)
min_per_seq	Minimum number of baits per each sequence in the database (e.g. chromosome, scaffold, etc.)
exclusions	Areas of the database to exclude
regions	Specific areas of the database to include
targets	Specific points of the database to include (e.g. SNPs)
regions.tiling	Choice of tiling for baits allocated in regions
targets.tiling	Choice of tiling for baits allocated in targets
regions.prop	Proportion of baits allocated in regions
targets.prop	Proportion of baits allocated in targets
seed	Seed to be set for a repeatable set of baits
restrict	Areas of the database to restrict the baits to
gc	Wished range of the proportion of the nucleotides G and C within the bait area
force	Option to request a very large number of baits to be generated

blast_baits()

The arguments for blast_baits() are:

Argument	Description
x	The input of _blast_baits(), which corresponds to the output from do_baits()
db	The database to blast the baits to
blastn_args	Additional parameters to pass to the blastn call