blatReadsVsRefs | R Documentation |
Make a 2bit file from one set of reads and blat another set against it
blatReadsVsRefs( reads, refs, outFile = NULL, faToTwoBit = "faToTwoBit", tmpDir = tempfile("dir"), ... )
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 |
NULL if outFile defined or an alignment data.frame if outFile is NULL
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