Hi 

I have a DNAStringset as..

A DNAStringSet instance of length 253
      width seq                                                                                                                names               
  [1]   601 TTTAGGATATTGCGGTTAGCATATGGGAATGGAAATAAGATATAATTGTATCATAG...AGAGATGGGCCATGGAGTGAAGTGGAATCTGAGAGTAGGGTAAGTTTGAGATGGT 1_450_1050_-_0
  [2]   601 TTATTTACGATGTACCTGTACATTGTGCAGAAGGTCTTCAGAGTGAGTTTAAGCTA...GAGGGAGCCAATGAGATTTTAAAGGGTATATTACTTATCTTATCGATAAGCAGTA 1_30718_31318_+_4...
  [3]   601 GTGTCGGTGGCACTTCTTTGCAATGTGACAAAAGTATTATTTTGATTGGCGGATTG...GGCACGACCTCCAGAGGGTGATTCAGTAAAAGAGAACAAAAAGGCAAGGAAGAGC 1_41760_42360_+_1...
  [4]   601 GCCATGAACAGGGAAGCAGAATTTGATTCGAAGACTAAGACCAAGCATACCCATTC...TTTCGGCTATCGGAGCCTTTGATTTAATCGCCGGTGCCTACGTCTTTGGTGTGTA 1_70117_70717_-_1...
  [5]   601 ATAAGTTCCACGTTAGTATTGTTGCTATCTGCCTTCCTTCGTAACTTAGTTCCCTA...GTCGTCAATGGTGGGTCTCTTCGGTACGCAACGGTTCAAAATACTCTTGATTAAC 1_124212_124812_-...

i want to put random bases at middle 20 positions of this DNAStringSet. Please suggest me some way to do this

.

Hi,

You can do something along these lines:

library(Biostrings)
dna <- DNAStringSet(c("ACGNACCATG", "ACANAAAATG", "ACGNATTTTT"))
dna
#   A DNAStringSet instance of length 3
#     width seq
# [1]    10 ACGNACCATG
# [2]    10 ACANAAAATG
# [3]    10 ACGNATTTTT

random_nucleotides <- sample(DNA_BASES, length(dna))
random_nucleotides
# [1] "G" "C" "T"

subseq(dna, start=4, width=1) <- random_nucleotides
dna
#   A DNAStringSet instance of length 3
#     width seq
# [1]    10 ACGGACCATG
# [2]    10 ACACAAAATG
# [3]    10 ACGTATTTTT

Cheers,

H.