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Designing Computational Biology Workflows with Perl
Conditional Remix & Share Permitted
CC BY-NC-SA
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This material introduces Linux File System structures and demonstrates how to use commands to communicate with the operating system through a Terminal program. Basic program structures and system() function of Perl are discussed. A brief introduction to gene-sequencing terminology and file formats are given.

Subject:
Applied Science
Computer Science
Material Type:
Lecture Notes
Provider:
CUNY Academic Works
Provider Set:
Queensborough Community College
Author:
Esma Yildirim
Yildirim Esma
Date Added:
05/01/2019
Designing Computational Biology Workflows with Perl
Conditional Remix & Share Permitted
CC BY-NC-SA
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This material introduces the AWS console interface, describes how to create an instance on AWS with the VMI provided, connect to that machine instance using the SSH protocol. Once connected, it requires the students to write a script to enter the data folder, which includes gene-sequencing input files and print the first five line of each file remotely. The same exercise can be applied if the VMI is installed on a local machine using virtualization software (e.g. Oracle VirtualBox). In this case, the Terminal program of the VMI can be used to do the exercise.

Subject:
Applied Science
Computer Science
Material Type:
Activity/Lab
Lecture Notes
Provider:
CUNY Academic Works
Provider Set:
Queensborough Community College
Author:
Esma Yildirim
Date Added:
06/04/2019
Designing Computational Biology Workflows with Perl
Conditional Remix & Share Permitted
CC BY-NC-SA
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This manual guides the instructor to combine the partial files of the virtual machine image and construct sequencer.ova file. It is accompanied by the partial files of the virtual machine image.

Subject:
Applied Science
Computer Science
Material Type:
Activity/Lab
Lecture Notes
Provider:
CUNY Academic Works
Provider Set:
Queensborough Community College
Author:
Esma Yildirim
Date Added:
06/04/2019
"Designing Computational Biology Workflows with Perl Part 2
Conditional Remix & Share Permitted
CC BY-NC-SA
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This material briefly reintroduces the DNA double Helix structure, explains SNP and INDEL mutations in genes and describes FASTA, FASTQ, BAM and VCF file formats. It also explains the index creation, alignment, sorting, marking duplicates and variant calling steps of a simple preprocessing workflow and how to write a Perl script to automate the execution of these steps on a Virtual Machine Image.

Subject:
Applied Science
Computer Science
Material Type:
Activity/Lab
Lecture Notes
Provider:
CUNY Academic Works
Provider Set:
Queensborough Community College
Author:
Esma Yildirim
Date Added:
06/04/2019
Designing Computational Biology Workflows with Perl Part 2b
Conditional Remix & Share Permitted
CC BY-NC-SA
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This material introduces the AWS console interface, describes how to create an instance on AWS with the VMI provided and connect to that machine instance using the SSH protocol. Once connected, it requires the students to write a script to automate the tasks to create VCF files from two different sample genomes belonging to E.coli microorganisms by using the FASTA and FASTQ files in the input folder of the virtual machine. The same exercise can be applied if the VMI is installed on a local machine using virtualization software (e.g. Oracle VirtualBox). In this case, the Terminal program of the VMI can be used to do the exercise.

Subject:
Applied Science
Computer Science
Material Type:
Activity/Lab
Lecture Notes
Provider:
CUNY Academic Works
Provider Set:
Queensborough Community College
Author:
Esma Yildirim
Date Added:
06/04/2019