Looking at reference transcriptome generated from NCBI.

    # Replace 'input.fasta' with the name of your multi-sequence fasta file
    input_file <- "/home/shared/8TB_HDD_02/cvaldi/celeste-tunicate-devo/data/sequence.fasta"
    sequences <- read.fasta(input_file)

Pulling 10 random sequences from that fasta 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]

Saving that info in an output.fasta file in the output directory.

    # Replace 'output.fasta' with your desired output file name
    output_file <- "../output/output.fasta"
    write.fasta(selected_sequences, names(selected_sequences), output_file, open = "w")

Using samtols faidx command to index the fasta file to used in
downstream IGV visualization.

    #needed downstream for IGV
    /home/shared/samtools-1.12/samtools faidx \
    ../output/output.fasta

Using the fuzznuc program to search for the pattern CG in the 10 random
sequences from the reference transcriptome file.

    fuzznuc -sequence ../output/output.fasta -pattern CG -rformat gff -outfile ../output/CGoutput.gff

After having run fuzznuc and produced a CG output file, we can push that
file to GitHub. This way we can read it into our local IGV software via
the GitHub URL.

You will also need to read in the reference genome or reference
transcriptome (fasta format) into IGV so we have something to compare
the CG motif output file to. I used the *Botryllus schlosseri* reference
transcriptome that I used in all my other analyses in this course.

Below are some screenshots of the IGV visualization of the CG motif file
we just made:

Close up:
![](https://github.com/course-fish546-2023/celeste-coursework/blob/main/assignments/close_up_igv.png?raw=true)

Birds eye view:
![](https://github.com/course-fish546-2023/celeste-coursework/blob/main/assignments/igv_panel.png?raw=true)