blat: Function to run BLAT.

View source: R/blat.R

blatR Documentation

Function to run BLAT.

Description

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.

Usage

blat(sequenceTb, database, blat_exec, min_score = 20)

Arguments

sequenceTb

data.frame, each row corresponding to one sequence to be queried using BLAT. The data frame consists of the following two columns:

qname

character, name/identifier of the query sequence.

seq

character, (nucleotide) sequence to be queried using BLAT.

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 minScore parameter in the command-line BLAT program (default: 20).


Fraternalilab/BrepConvert documentation built on Oct. 14, 2022, 5:54 p.m.