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Follow-up Amazon & Unix Konrad Paszkiewicz. 9am – 10:30am Continue with Unix (and/or Perl tutorial) Open the text file containing your Amazon password.

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Presentation on theme: "Follow-up Amazon & Unix Konrad Paszkiewicz. 9am – 10:30am Continue with Unix (and/or Perl tutorial) Open the text file containing your Amazon password."— Presentation transcript:

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 10:15 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 and sort them by column 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 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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