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bash-beginners [2019/01/15 04:22]
telatina
bash-beginners [2019/03/12 03:57] (current)
telatina
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 ==== Day1: The first tour ==== ==== Day1: The first tour ====
-**January 21, Mon**+ 
  
 A **[[bash-first|brief introduction]]** to the core concepts of the command line as a good environment for bioinformatics analysis. A hands-on tutorial to log in into a remote Linux server using each participants laptop, and test the first commands. A **[[bash-first|brief introduction]]** to the core concepts of the command line as a good environment for bioinformatics analysis. A hands-on tutorial to log in into a remote Linux server using each participants laptop, and test the first commands.
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     - A command line text editor: ''​nano''​     - A command line text editor: ''​nano''​
 ==== Day 2: basic commands ==== ==== Day 2: basic commands ====
-**January 23, Wed**  + 
 **[[bash-second|Understanding the "file system"​]]**,​ relative and absolute paths, and the commands to organize the directories,​ to list files, to copy and move files and directories. Introduction to commands to interact with text files and view them. **[[bash-second|Understanding the "file system"​]]**,​ relative and absolute paths, and the commands to organize the directories,​ to list files, to copy and move files and directories. Introduction to commands to interact with text files and view them.
 We will use the **FASTA** and **FASTQ** file formats as examples. We will use the **FASTA** and **FASTQ** file formats as examples.
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     - Redirecting a command output into a text file     - Redirecting a command output into a text file
 ==== Day 3: Extracting data from text files ==== ==== Day 3: Extracting data from text files ====
-**TBD**+ 
  
 Using terminal commands to **[[bash-3|interact with bioinformatics files]]**. We'll introduce the SAM file format used to store NGS mapping, the VCF format (for SNP calling), and some tabular annotation files (**GFF**, **GTF**). Using terminal commands to **[[bash-3|interact with bioinformatics files]]**. We'll introduce the SAM file format used to store NGS mapping, the VCF format (for SNP calling), and some tabular annotation files (**GFF**, **GTF**).
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 ====  Day 4: The bioinformatician'​s perspective ==== ====  Day 4: The bioinformatician'​s perspective ====
-**TBD**+ 
  
 Using **[[bash-4|short reads alignment]]** as a theme, we'll introduce how to install new software to be used from the command line, users and file permissions,​ and of course the alignment program **bwa** and **samtools** the swiss army knife to manipulate SAM files. Using **[[bash-4|short reads alignment]]** as a theme, we'll introduce how to install new software to be used from the command line, users and file permissions,​ and of course the alignment program **bwa** and **samtools** the swiss army knife to manipulate SAM files.