blat | R Documentation |
This function invokes BLAT from the command line to search sequences given in sequenceTb
, against FASTA sequences stored in the file database
. The parameters used are: -out=blast8 -tileSize=6 -stepSize=1
, and minScore
given by the parameter min_score
of this function. The results are written to a temporary file and then read in as a data frame.
blat(sequenceTb, database, blat_exec, min_score = 20)
sequenceTb |
data.frame, each row corresponding to one sequence to be queried using BLAT. The data frame consists of the following two columns:
|
database |
character, filepath to the FASTA file storing the sequence database to be searched against using BLAT. |
blat_exec |
character, filepath to the executable of the BLAT program. |
min_score |
integer, minimum score to trigger a BLAT alignment, i.e. the |
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