ROPES summer school - CRG - May 2023
About the course
Introduction to Linux
Containers
Nextflow
Master of Pores 2
ROPES summer school - CRG - May 2023
ROPES summer school - CRG - May 2023
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ROPES summer school - CRG - May 2023
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Contents:
About the course
Outline
Learning objectives
Prerequisite / technical requirements
Dates, time, location
Program
Introduction to Linux
What is Linux?
What is a Command Line Interface (GUI)?
Create directory and practice moving around
Download files from repositories
Manipulate files, piping, parsing, reformatting
Sequence file formats: Fasta and fastq
Bed format and regular expressions
Space in volumes and permissions
Containers
Linux containers
Docker
Singularity
Nextflow
What is Nextflow?
What is Nextflow for?
Main advantages
Workflow structure
Installation
Channels and Operators
Exercise
Processes
Workflow
Master of Pores 2
Basics of Direct RNA Sequencing (DRS)
Master Of Pores 2 (MOP2) - preprocessing and polyA tail estimation (1)
Hands-on 1:
mop_preprocess
and
mop_tail
Master Of Pores 2 (MOP2) - RNA modification detection (2)
Hands-on 2:
mop_mod
and
mop_consensus