Please note, the isPcr command line program explains how to use it if you run it without arguments. Its usage message is listed below.
--Hiram Manisha Brahmachary wrote: > Hello, > > I want to run a batch query for insilicoPCR. I have downloaded the > blatSuite.33x5.zip from http://hgwdev.cse.ucsc.edu/~kent/exe/. > > Can you please send me a README.txt for the various steps to do the insilico > PCR on command line. > > The usage.txt doesnot give the sequential steps on needs to do to do the > command line insilicoPCR . > > Thanks a lot. > > Manisha isPcr - Standalone v 34x4 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. options: -ooc=N.ooc Use overused tile file N.ooc. N should correspond to the tileSize -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. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
