TAPseqInput {TAPseq} | R Documentation

## Create TAPseq input from target sequences

### Description

This function creates input for TAP-seq primer design from a DNAStringSet containing the target sequences (typically transcript sequences).

### Usage

    TAPseqInput(
      target_sequences,
      product_size_range,
      beads_oligo = NA,
      reverse_primer = "CTACACGACGCTCTTCCGATCT",
      target_annot = NULL,
      primer_num_return = 5,
      min_primer_region = 100,
      primer_opt_tm = 63,
      primer_min_tm = 59,
      primer_max_tm = 66
    )

### Arguments

`target_sequences` | A named `DNAStringSet` object containing all target sequences.
`product_size_range` | Numerical vector of length 2 specifying the desired length of the resulting amplicons.
`beads_oligo` | Beads-oligo-dT sequence for the used droplet sequencing protocol (10x, Drop-seq). If nothing is specified (`beads_oligo = NA`), the 10x V3 Beads-oligo-dT sequence is used. Can be changed if primers are for instance designed for Drop-seq. Any barcode bases need to be replaced by `N`.
`reverse_primer` | Reverse primer sequence used for all PCR reactions. Default is the 10x primer sequence: `CTACACGACGCTCTTCCGATCT`.
`target_annot` | (optional) A named `GRangesList` object with transcript annotations in case the targets are transcripts of gene loci. If provided, each `GRanges` within the list should contain all exons of one targeted transcripts. Names need to be the same as for `target_sequences`.
`primer_num_return` | How many forward primers should be designed? (default: 5)
`min_primer_region` | Minimum sequence length required for primer design. Mostly relevant in case a sequence template is too short to allow the specified `product_size_range`.
`primer_opt_tm, primer_min_tm, primer_max_tm` | Optimal, minumum and maximum primer melting temperature. Set to NA to use Primer3s default values.

### Value

`TsIOList` object.

### Examples

    # chromosome 11 truncated transcript sequences and annotations
    data("chr11_truncated_txs_seq")

    # create TsIOList object for primer design from target sequences
    obj <- TAPseqInput(chr11_truncated_txs_seq, product_size_range = c(350, 500))
    obj

    # transcript annotations can be added for optional genome browser tracks of designed primers
    data("chr11_truncated_txs")
    obj <- TAPseqInput(chr11_truncated_txs_seq, product_size_range = c(350, 500),
                       target_annot = chr11_truncated_txs)

    # create input for primer design with Drop-seq instead of default 10x
    ds_oligo <- "TTTTTTTAAGCAGTGGTATCAACGCAGAGTACNNNNNNNNNNNNNNNNNNNNTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT"
    ds_rev_primer <- "AAGCAGTGGTATCAACGCAGAGT"
    ds_obj <- TAPseqInput(chr11_truncated_txs_seq, beads_oligo = ds_oligo,
                          reverse_primer = ds_rev_primer, product_size_range = c(350, 500),
                          primer_opt_tm = 62, primer_min_tm = 57, primer_max_tm = 65)

[Package TAPseq version 0.99.6 Index]