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Follow-up Amazon & Unix

Follow-up Amazon & Unix. Konrad Paszkiewicz. 9am – 10:30am. 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

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Follow-up Amazon & Unix

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  1. Follow-up Amazon & Unix Konrad Paszkiewicz

  2. 9am – 10:30am • 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 10:15before 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 and sort them bycolumn 3 • Q4. How many types of feature are there in the At_genes.gff file ? (Hint: this is in Column 3 – how many CDS, exon, mRNA etc entries are there?)

  9. Answers • Q1. • grep "^>" intron_IME_data.fasta • 59260 • Q2. • grep –c "^>.*GTP" At_proteins.fasta • 246 • Q3. • grep Chr5 At_genes.gff | sort –k 3 • Q4. - cut -f 3 At_genes.gff | sort | uniq -c

  10. When to use Perl GFF file FASTA file

  11. After coffee • Jose and Dan • QIIME • You will be using a different AMI so please terminate your current instances

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