update challenges to callouts

demo-genome-assembly.qmd

@@ -1,9 +1,12 @@
 # Genome assembly
 
+::: {.callout-warning}
 ## Challenge {.unnumbered}
 Your professor has sequenced a bacterial isolate using PacBio and Nanopore sequencing methods and has got the FASTQ files from both technologies. Now he needs to know the quality and quantity of these data before start any other analysis and ask you to assess the data. He needs to know how many sequences there are, how many base pairs (in GB) are there and the N50. He is also interested in see a visualization of the i) number of bases vs. sequence lengths (log transformed) and ii) the read length vs. read quality vs. read number.
 
 He ask you to document every step and to conclude what data should be used.
+:::
+
 
 
 ## Download the reads {.unnumbered}

demo-genome-searching.qmd

@@ -1,8 +1,10 @@
 # Genome searching
 
-
+::: {.callout-warning}
 ## Challenge {.unnumbered}
 Your profesor is interested on knowing how many  complete genomes of Bacillus subtilis are there in the NCBI databases. He ask you later to count the number of features (genes, CDS, ncRNA, rRNA, etc.) in the genome of Bacillus subtilis NCIB 3610 (GCF_002055965.1). And tell you to document each of the steps and how did you end up with the answer. Saving the file with your initials (e.g., CG-activity01.{md,txt,docx})
+:::
+
 
 ### Downloading a genome {.unnumbered}
 

demo-phylogenetics.qmd

@@ -1,8 +1,10 @@
 # Phylogenetic analysis
 
-
+::: {.callout-warning}
 ## Challenge {.unnumbered}
 Your professor has been working with some mammal species and want to know the relationships of some sampled individuals. To do so he extracted the DNA and amplified the mitochondrial CYTB gene of those individuals. He gives a folder with multiple sequences and ask you to align them and to reconstruct two trees one using maximum likelihood (ML) and other using a Bayesian inference (BI). Then ask you to explain if both trees are congruent with each other.
+:::
+
 
 ## Sequence alignment *cytb* {.unnumbered}
 

demo-reads-assessment.qmd

@@ -1,8 +1,10 @@
 # Sequence reads assesment
 
+::: {.callout-warning}
 ## Challenge {.unnumbered}
 Your professor challenges you to assembly a bacterial genome.
 He wants to know if  an assembly using Illumina reads or Nanopore reads is better. The raw sequences for Illumina could be downloaded with the code SRR15634574. And the Nanopore raw reads with SRR15634573 here: https://sra-explorer.info. Choose at least on set and follow the instruction from the lecture to assemble the genome. Document each step and send to the professor the `assembly-{your-initials}.fasta`. You could form groups of max. 4 students.
+:::
 
 
 ## General stats from fastq files {.unnumbered}

demo-sanger-processing.qmd

@@ -1,9 +1,11 @@
 # Sanger processing
 
+::: {.callout-warning}
 ## Challenge {.unnumbered}
-
 Your professor gives you a couple of .ab1 files of a 16S rRNA gene from an old project a student conducted. She tells you to process and analyse them using the Sanger sequence pipeline analysis. And as she doesn't know from which species they belong, she ask you to identify the organism to whom it belongs by using the resulting consensus sequence. She finally reminds you to document each step of the process including the identification step.
 
+:::
+
 ## Processing a single `.ab1` pair {.unnumbered}
 
 ```{r}