designOligoPool: Design oligo pool by tiling a set of sequences
In cshukla/oligoGames: Analyze data from massively parallel reporter assays

Description Usage Arguments Examples

View source: R/designOligoPool.R

This function helps a user design an oligo pool based on their needs. Many different options provided to the user allow a high degree of customization and flexibility. There are 3 main steps in this function: (1). Generate a potential set of barcodes avoiding the presence of any unwanted sub strings such as microRNA seeds (2) Tile each sequence in the input file using the specified tile size and overlap (3) Generate final oligo pool by concatenating the universal primers, potential restriction enzyme sequence and a unique barcode with each tile. Each oligo is designed as UPS_FP—-VarSeq—-RESite—-Barcode—-UPS_RP

designOligoPool(regionsFile, tileSize = 110, overlap = 10,
  barcodesPerSequence = 1, barcodesFile = "",
  univPrimers = c("ACTGGCCGCTTCACTG", "AGATCGGAAGAGCGTCG"), reSeq = "",
  microSeedsFile, badNucs = c("AAA", "TTT", "CCC", "GGG"), numScrambles = 0,
  barcodeLen = 10, outDir = "lncTilingGame")

`regionsFile`	the name of the file with regions to tile for the oligo pool. Please make sure the file is in FASTA format and has unique headers for sequence of each region
`tileSize`	numeric indicating the size of each individual oligo. The tile size is also sometimes called the length of variable sequence. Since universal primer sites, barcodes and potentially a Restriction Enzyme site has to be added to the tile for a complete oligo, it is usually ~50 bp less than the maximum length of the oligo you can synthesize. Default value is 110
`overlap`	numeric describing how many nucleotides you wish to move between 2 successive tiles. Sometimes, this is called the step size and this number will determine the resolution of your data downstream. Default value is 10
`barcodesPerSequence`	numeric for the number of unique barcodes to use for each variable sequence. In certain applications, the user might wish to use upto 20 barcodes for each individual tile for more accurate measurement. Default value is 1
`barcodesFile`	the name of the file with a list of barcodes you wish to use for designing the oligo pool. You don't need to give this file since the script can generate barcodes on its own but is given to the user as an option. If you provide the file, please note `microSeedsFile` and `badNucs` are redundant. Default value is NULL
`univPrimers`	character vector of the universal primer sequences added upstream and downstream in each oligo. Provide in the order c('ForwardPrimer', 'ReversePrimer'). Default value is c('ACTGGCCGCTTCACTG','AGATCGGAAGAGCGTCG'). Use non-standard primer sequences at your own risk
`reSeq`	character describing the restriction enzyme site you wish to add. To play some games, a restriction enzyme site is neccessary but this is not strictly required. Defaults to ”
`microSeedsFile`	the name of a file with microRNA seeds. These sequences are required to ensure they are not present in any barcodes. Please ensure the file is gzipped and contains one microRNA seed sequence per line. This is a required parameter if `barcodeFile` is not given.
`badNucs`	character vector with potential sub strings you wish to avoid in barcodes. For example, triple N's are hard to PCR and so it is a good idea to avoid them in barcodes. This option is highly recommended if `barcodeFile` is not specified. Default value is c('AAA','TTT', 'CCC', 'GGG')
`numScrambles`	numeric describing the number of times each tile (variable sequence) should be scrambled. Default is 0
`barcodeLen`	numeric describing the length of the barcode. Default value is 10
`outDir`	the name of a directory you want to write the oligo pool sequences to. The directory will be created if not present already. Default value is lncTilingGame

## Not run: 
regionsFile <- system.file("extdata", "testRegions.fa", package='oligoGames')
microSeedsFile <- system.file('extdata', 'hg19miRSeeds.txt.gz', package='oligoGames')
outDir <- 'demoOligoGame'
designOligoPool(regionsFile = regionsFile, tileSize = 110, overlap = 10, 
barcodesPerSequence = 1, barcodesFile = '', microSeedsFile = microSeedsFile, 
reSeq = '', numScrambles = 0, barcodeLen = 10, outDir = outDir)

## End(Not run)