blatReadsVsRefs: Make a 2bit file from one set of reads and blat another set...

In sherrillmix/dnar: Miscellaneous functions to deal with bioinformatic analyses

Make a 2bit file from one set of reads and blat another set against it

Description

Make a 2bit file from one set of reads and blat another set against it

Usage

blatReadsVsRefs(
  reads,
  refs,
  outFile = NULL,
  faToTwoBit = "faToTwoBit",
  tmpDir = tempfile("dir"),
  ...
)

Arguments

reads	vector of query reads with names
refs	vector of reference reads with names
outFile	file to write blat to (if ends in .gz then isGz defaults to true and writes to gzipped file). If NULL then output to temp file, read in and return.
faToTwoBit	path to faToTwoBit program from blat
tmpDir	directory to store working files
...	additional arguments to run blat

Value

NULL if outFile defined or an alignment data.frame if outFile is NULL

sherrillmix/dnar documentation built on July 18, 2022, 10:07 p.m.