updating year

biocorecrg · Oct 21, 2024 · 9dcfd63 · 9dcfd63
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diff --git a/docs/alignment.md b/docs/alignment.md
@@ -39,7 +39,7 @@ cd .. # go up one level to the root of the project, if needed
 mkdir alignment
 cd alignment
 
-wget https://biocorecrg.github.io/PhD_course_genomics_format_2023/data/H3K4me1.sam.gz
+wget https://biocorecrg.github.io/PhD_course_genomics_format_2024/data/H3K4me1.sam.gz
 gunzip H3K4me1.sam.gz
 
 more H3K4me1.sam 
@@ -93,7 +93,7 @@ To convert SAM to BAM, sort, index, etc. you can use the program: [**samtools**]
 
 
 ```{bash}
-wget https://biocorecrg.github.io/PhD_course_genomics_format_2023/data/H3K4me1.bam
+wget https://biocorecrg.github.io/PhD_course_genomics_format_2024/data/H3K4me1.bam
 
 ```
 

diff --git a/docs/fasta_format.md b/docs/fasta_format.md
@@ -51,7 +51,7 @@ cd ../ # to go to the root of the project folder, if needed
 mkdir db
 cd db
 
-wget https://biocorecrg.github.io/PhD_course_genomics_format_2023/data/Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz
+wget https://biocorecrg.github.io/PhD_course_genomics_format_2024/data/Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz
 ```
 
 The genome is generally represented as a FASTA file (.fa file). Each chromosome sequence starts with a header row, starting with "**>**":
@@ -182,7 +182,7 @@ The flow of commands is the following:
 
 **EXERCISE**
 
-Download in the folder ./db the annotation file at https://biocorecrg.github.io/PhD_course_genomics_format_2023/data/annotation.gtf.gz  
+Download in the folder ./db the annotation file at https://biocorecrg.github.io/PhD_course_genomics_format_2024/data/annotation.gtf.gz  
  * What is the date of this file? (use command **more** to explore the file)
  * How many lines in this file?
  * How many lines in this file contain the word "HAVANA"?

diff --git a/docs/fastq.md b/docs/fastq.md
@@ -47,10 +47,10 @@ It is recommended to always use the date at the beginning of the folder name, in
 <br>
 
 ```{bash}
-mkdir 2023-10-25-genomics_data_formats
+mkdir 2024-10-25-genomics_data_formats
 
 # type cd 2[TAB] to autofill the folder name
-cd 2023-10-25-genomics_data_formats
+cd 2024-10-25-genomics_data_formats
 ```
 
 <br>
@@ -61,7 +61,7 @@ Let's use command **cat** to create a simple README.txt
 
 ```{bash}
 cat > README.txt
-Date: 25/10/2023
+Date: 25/10/2024
 Author: ....
 Project title: This is my first project.
 ```
@@ -108,7 +108,7 @@ Here my suggestion in case you might want to try **VIM**
 Download a **test dataset** by executing the command **wget**:
 
 ```{bash}
-wget https://biocorecrg.github.io/PhD_course_genomics_format_2023/data/H3K4me1_chr21.fq.gz 
+wget https://biocorecrg.github.io/PhD_course_genomics_format_2024/data/H3K4me1_chr21.fq.gz 
 --2019-10-15 14:42:59--  https://biocorecrg.github.io/PhD_course/data/H3K4me1_chr21.fq.gz
 Resolving biocorecrg.github.io (biocorecrg.github.io)... 185.199.109.153, 185.199.111.153, 185.199.110.153, ...
 Connecting to biocorecrg.github.io (biocorecrg.github.io)|185.199.109.153|:443... connected.
@@ -134,7 +134,7 @@ ls -lh H3K4me1_chr21.fq.gz
 <br/>
 
 **EXERCISE**<br/>
-* Download the **control file for this ChIP-seq experiment** at https://biocorecrg.github.io/PhD_course_genomics_format_2023/data/input_chr21.fq.gz <br>
+* Download the **control file for this ChIP-seq experiment** at https://biocorecrg.github.io/PhD_course_genomics_format_2024/data/input_chr21.fq.gz <br>
 * What is the size of the input file?
 * Look up for the options of the command **ls** using the command **man ls**. 
 * Which option in command **ls** allows to display files sorted by size? Run this command.

diff --git a/docs/genome_browser.md b/docs/genome_browser.md
@@ -47,7 +47,7 @@ You can also display aligned sequences, but you need to place your sorted and in
 Copy paste this link into the **custom track**. This is the sorted version of our alignment, hosted in the github web-server.
 
 ```{bash}
-https://biocorecrg.github.io/PhD_course_genomics_format_2023/data/H3K4me1_s.bam
+https://biocorecrg.github.io/PhD_course_genomics_format_2024/data/H3K4me1_s.bam
 ```
 
 In the same place we also hosted the index, called **H3K4me1_s.bam.bai**. When you don't specify it, the browser will automatically look for the index just adding **.bai** ad the end of the link we provide.

diff --git a/docs/index.md b/docs/index.md
@@ -4,7 +4,7 @@ title: Home
 navigation: 1
 ---
 
-# ![logo](https://raw.githubusercontent.com/CRG-CNAG/BioCoreMiscOpen/master/logo/biocore-logo_small.png) PhD Course 2023
+# ![logo](https://raw.githubusercontent.com/CRG-CNAG/BioCoreMiscOpen/master/logo/biocore-logo_small.png) PhD Course 2024
 
 # Linux commands and Genomics data formats for biologists
 
@@ -19,7 +19,7 @@ navigation: 1
 
 from the CRG [Bioinformatics core facility](https://biocore.crg.eu/) (office 425, 4th floor of the hospital side)
 
-Materials for the course are available at [this website](https://biocorecrg.github.io/PhD_course_genomics_format_2023/).
+Materials for the course are available at [this website](https://biocorecrg.github.io/PhD_course_genomics_format_2024/).
 
 
 ##  Learning objectives

diff --git a/docs/peak_calling.md b/docs/peak_calling.md
@@ -37,7 +37,7 @@ cd ..
 mkdir peaks
 cd peaks
 
-wget https://biocorecrg.github.io/PhD_course_genomics_format_2023/data/H3K4me_peaks.xls
+wget https://biocorecrg.github.io/PhD_course_genomics_format_2024/data/H3K4me_peaks.xls
 
 
 more H3K4me_peaks.xls
@@ -81,7 +81,7 @@ chr	start	end	length	abs_summit	pileup	-log10(pvalue)	fold_enrichment	-log10(qva
 Another output file is **H3K4me_peaks.narrowPeak**, which, as you can see contains the information only about peaks. This is a BED file.
 
 ```{bash}
-wget https://biocorecrg.github.io/PhD_course_genomics_format_2023/data/H3K4me_peaks.narrowPeak
+wget https://biocorecrg.github.io/PhD_course_genomics_format_2024/data/H3K4me_peaks.narrowPeak
 
 more H3K4me_peaks.narrowPeak
 21	6565480	6565885	H3K4me_peak_1	32	.	3.66432	7.98323	3.26622	153

diff --git a/docs/qc.md b/docs/qc.md
@@ -26,15 +26,15 @@ cd .. # make sure to move up in the root of the project folder
 mkdir fastqc
 cd fastqc
 
-wget https://biocorecrg.github.io/PhD_course_genomics_format_2023/data/H3K4me1_chr21_fastqc.html
+wget https://biocorecrg.github.io/PhD_course_genomics_format_2024/data/H3K4me1_chr21_fastqc.html
 
 firefox H3K4me1_chr21_fastqc.html
 ```
 
 **NOTE**. If you don't have X11 forwarding, don't worry. Just copy paste this link in your browser:
 
 ```{bash}
- https://biocorecrg.github.io/PhD_course_genomics_format_2023/data/H3K4me1_chr21_fastqc.html
+ https://biocorecrg.github.io/PhD_course_genomics_format_2024/data/H3K4me1_chr21_fastqc.html
 ```
 
 <img src="images/fastqc.png" width="800"/>