Markdown is a simple way to write formatted text using a plain text file (with extension .md). We use it for this website, and you will use it for your notebook.md.

For each element below you will find the text you type and the result.

Headings

# Title
## Section
### Subsection

Use # for the title, ## for sections, ### for subsections (one # more for each level). Always leave a space after the #.

Paragraphs and line breaks

This is the first paragraph.
This is also part of the first paragraph.

This is the second paragraph: only a blank line separates paragraphs.

This is the first paragraph. This is also part of the first paragraph.

This is the second paragraph: only a blank line separates paragraphs.

A single line break in the text does not create a new line in the result: leave an empty line, or end the line with two spaces.

Bold, italic and inline code

This is **bold**, this is *italic*, and this is ***both***.
The species name is *Escherichia coli*.
Run the command `seqfu stats` on the file `reads.fastq.gz`.

This is bold, this is italic, and this is both. The species name is Escherichia coli. Run the command seqfu stats on the file reads.fastq.gz.

Lists

* First item
* Second item
  * A nested item (indent with two spaces)
* Third item

1. First step
2. Second step
3. Third step

• First item
• Second item
  • A nested item (indent with two spaces)
• Third item

1. First step
2. Second step
3. Third step

Code blocks

Put your code between three backticks, and (optionally) write the language after the first three backticks:

```bash
cd /shared/team/2026_training/week2/{firstname}
seqfu stats --basename reads/*.fastq.gz > stats.tsv
```

cd /shared/team/2026_training/week2/{firstname}
seqfu stats --basename reads/*.fastq.gz > stats.tsv

Use this for commands and for file contents: it keeps the spacing and prevents characters like * or _ from being interpreted as formatting.

Links and images

[Seqfu documentation](https://telatin.github.io/seqfu2/)

![Alternative text](figure.png)

Seqfu documentation

An image is a link preceded by !. The image file must be reachable from the page (for example in the same directory).

Quotes

> What differences do you notice between the two datasets?

What differences do you notice between the two datasets?

We use quotes for questions and notes.

Tables

Tables in markdown are “drawn” with pipes (|) and dashes (-) like so:

Sample | Reads | Organism
-------|-------|---------
DTP1-1 | 2.9 M | Yeast
DTP1-2 | 3.1 M | Lambda

The line of dashes after the first row is required. The columns do not need to be aligned in the text file.

Horizontal line

---

Checklists

- [x] Create the notebook
- [ ] Create the conda environment

• Create the notebook
• Create the conda environment

Escaping

To show a special character literally, put a backslash before it:

2 \* 3 = 6, and file\_name.txt

2 * 3 = 6, and file_name.txt

A minimal notebook example

# Week 2 notebook

## Read counts

Command used:

```bash
seqfu stats --basename reads/lab/*.fastq.gz > seqfu-stats/illumina.tsv
```

Observations:

* 32 files, 16 samples
* **R1** and **R2** have the same number of reads

> Question: which sample has the fewest reads?
> Answer: *to be checked*

Quick reference