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Computational pipelines
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Computational pipelines
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Academic year 2023/2024
- Course ID
- NEU0293B
- Teacher
- Davide Marnetto (Lecturer)
- Year
- 2nd year
- Teaching period
- First semester
- Type
- Related or integrative
- Credits/Recognition
- 2
- Course disciplinary sector (SSD)
- BIO/11 - molecular biology
- Delivery
- Formal authority
- Language
- English
- Attendance
- Optional
- Type of examination
- Practice test
- Type of learning unit
- modulo
- Modular course
- Applied bioinformatics (NEU0293)
- Prerequisites
- Theoretical knowledge of molecular biology concepts and high-throughput analyses such as DNA and RNA sequencing. Basic knowledge of programming notions, such as: file system, commands, variables, control flow (if/else/loops), lists, functions.
It is necessary to master the concepts seen in the modules of Programming and Bioinformatic of the Data Science teaching.
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Sommario del corso
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Course objectives
Please refer to the integrated course.
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Results of learning outcomes
Please refer to the integrated course.
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Program
- Pipeline organizing principles, introduction to Python Snakemake. Conda environments and portability. Installation of Conda and Snakemake.
- Introduction to rules (input, output, shell), rule dependency. First pipeline of 2 example rules.
- Snakemake options and wildcards. Testing and debugging the example pipeline.
- Pipeline automatization, wildcards, expand, “all” rules. Fastq quality control rules.
- Pipeline generalization, configuration files. Rules to map fastqs and obtain bam.
- Advanced pipelines with parameters, output attributes, rule priorities. Aligment quality control rules
- Exploiting computational resources: parallelization, Memory resources. expression quantification rules
- Snakemake is Python. Python basics, functions as input. Rules for the analysis of gene expression
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Course delivery
Please refer to the integrated course.
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Learning assessment methods
The learning assesment is ingertated with the other module of the curse. See the relative page.
The students should produce one integrated report concerning both modules and there will be one intergated oral examination.
Suggested readings and bibliography
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