TAPseqInput {TAPseq} | R Documentation |
This function creates input for TAP-seq primer design from a DNAStringSet containing the target sequences (typically transcript sequences).
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 )
target_sequences |
A named |
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 ( |
reverse_primer |
Reverse primer sequence used for all PCR reactions. Default is the 10x
primer sequence: |
target_annot |
(optional) A named |
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 |
primer_opt_tm, primer_min_tm, primer_max_tm |
Optimal, minumum and maximum primer melting temperature. Set to NA to use Primer3s default values. |
TsIOList
object.
# 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)