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Follow-Up Tutorial: Working with AWS, Unix, and Arabidopsis Data Analysis

Join us for a follow-up session where we continue our exploration of Unix and Perl. We'll access your Amazon account to start your instance. Remember, your public DNS address for the VM has likely changed, so be prepared to update it. We'll have a short challenge at 9:50 AM to test your knowledge before coffee. After logging in, you will work with Arabidopsis data files to answer specific questions regarding sequences and proteins. Bring your problem-solving skills and let's enhance our bioinformatics capabilities!

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Follow-Up Tutorial: Working with AWS, Unix, and Arabidopsis Data Analysis

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  1. Follow-up Amazon & Unix Konrad Paszkiewicz

  2. 9am – 10am • Continue with Unix (and/or Perl tutorial) • Open the text file containing your Amazon password from yesterday • Go to https://nescent.signin.aws.amazon.com/console • Start your instance • Remember that your public DNS address for the VM will have changed • Short 10 min challenge at 09:50 before coffee

  3. After Log-In

  4. Start your instance

  5. Copy the new Host DNS address

  6. Start the NoMachine Program

  7. Paste the DNS address

  8. Quiz! • Use files in: ~/tutorial_materials/Data/Arabidopsis • Q1. How many sequences are listed in the file intron_IME_data.fasta ? • Q2. How many proteins with names containing the word GTP are in the file At_proteins.fasta ? • Q3. Print every entry on Chromosome 5 in At_genes.gff in order of column 3

  9. Answers • Q1. • grep "^>" intron_IME_data.fasta • 59260 • Q2. • grep –c "^>.*GTP" At_proteins.fasta • 246 • Q3. • grep Chr5 At_genes | sort –k 3

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