isPcr - Standalone v 33x2 In-Situ PCR Program usage:
isPcr database query output
where database is a fasta, nib, or twoBit file or a text file containing
a list of these files, query is a text file file containing three columns: name,
forward primer, and reverse primer, and output is where the results go.
The names 'stdin' and 'stdout' can be used as file names to make using the
program in pipes easier.
-ooc=N.ooc Use overused tile file N.ooc. N should correspond to
-tileSize=N the size of match that triggers an alignment.
Default is 11 .
-stepSize=N spacing between tiles. Default is 5.
-maxSize=N - Maximum size of PCR product (default 4000)
-minSize=N - Minimum size of PCR product (default 0)
-minPerfect=N - Minimum size of perfect match at 3' end of primer (default 15)
-minGood=N - Minimum size where there must be 2 matches for each mismatch (default 15)
-mask=type Mask out repeats. Alignments won't be started in masked region
but may extend through it in nucleotide searches. Masked areas
are ignored entirely in protein or translated searches. Types are
lower - mask out lower cased sequence
upper - mask out upper cased sequence
out - mask according to database.out RepeatMasker .out file
file.out - mask database according to RepeatMasker file.out
-makeOoc=N.ooc Make overused tile file. Database needs to be complete genome.
-repMatch=N sets the number of repetitions of a tile allowed before
it is marked as overused. Typically this is 256 for tileSize
12, 1024 for tile size 11, 4096 for tile size 10.
Default is 1024. Only comes into play with makeOoc
-flipReverse Reverse complement reverse (second) primer before using
-out=XXX - Output format. Either
fa - fasta with position, primers in header (default)
bed - tab delimited format. Fields: chrom/start/end/name/score/strand
psl - blat format.