Week 07: CG Motifs

Rpubs link:

# first install `seqinr` if not already on machine!
# install.packages("seqinr")

library(seqinr)

# Replace 'input.fasta' with the name of your multi-sequence fasta file
input_file <- "~/liz-rockfish/assignments/data/test_R1_seq_lib01.fasta"
sequences <- read.fasta(input_file)

# Set the seed for reproducibility (optional)
set.seed(42)

number_of_sequences_to_select <- 10

if (length(sequences) < number_of_sequences_to_select) {
  warning("There are fewer than 10 sequences in the fasta file. All sequences will be selected.")
  number_of_sequences_to_select <- length(sequences)
}

selected_indices <- sample(length(sequences), number_of_sequences_to_select)
selected_sequences <- sequences[selected_indices]

# Replace 'output.fasta' with your desired output file name
output_file <- read.fasta("~/liz-rockfish/assignments/output/10-seqs.fasta")

write.fasta(sequences = selected_sequences, names = selected_sequences, file.out = write_fasta_out, open = "w")

#likely will not need; fix issue where gff and fa name did not match
sed -i 's/>lcl|/>/g' ~/liz-rockfish/assignments/output/10-seqs.fasta

Create an index of our 10-seqs file

#needed downstream for IGV
/home/shared/samtools-1.12/samtools faidx \
~/liz-rockfish/assignments/output/10-seqs.fasta

Check out the rests of the index creation

head -1 ~/liz-rockfish/assignments/output/10-seqs.fasta.fai

A01335:621:H5WGLDSXF:3:1101:31494:4116  159 40  60  61

Time to use fuzznuc to find CG motifs!

fuzznuc -sequence ~/liz-rockfish/assignments/output/10-seqs.fasta -pattern CG -rformat gff -outfile ~/liz-rockfish/assignments/output/CGoutput.gff

Search for patterns in nucleotide sequences