> For the complete documentation index, see [llms.txt](https://ycl6.gitbook.io/guide-to-rna-seq-analysis/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://ycl6.gitbook.io/guide-to-rna-seq-analysis/preparations/obtain-sequencing-data.md).

# Obtain sequencing data

## Real-world RNA-seq data

This tutorial will use the dataset published by [Hannah R. Parker](https://doi.org/10.1080/15592294.2018.1543504) on sessile serrated adenomas/polyps

### Raw reads

We will retreieve the raw data from ArrayExpress [E-MTAB-6951](https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-6951)

```bash
$ cd /home/USER/SSAPs
$ mkdir fastqs
$ cd fastqs
```

Download `download.sh` , place in the `fastqs` folder and execute the file using `sh download.sh`

{% file src="/files/-M5Wt6Z88-tlJNusrT0y" %}
download.sh
{% endfile %}

This will download the paired-end fastqs of the 10 pairs of 0-IIa pre-lesion and adjacent normal tissue samples

```bash
$ ls *gz
ERR2675454_1.fastq.gz  ERR2675465_1.fastq.gz  ERR2675478_1.fastq.gz
ERR2675454_2.fastq.gz  ERR2675465_2.fastq.gz  ERR2675478_2.fastq.gz
ERR2675455_1.fastq.gz  ERR2675468_1.fastq.gz  ERR2675479_1.fastq.gz
ERR2675455_2.fastq.gz  ERR2675468_2.fastq.gz  ERR2675479_2.fastq.gz
ERR2675458_1.fastq.gz  ERR2675469_1.fastq.gz  ERR2675480_1.fastq.gz
ERR2675458_2.fastq.gz  ERR2675469_2.fastq.gz  ERR2675480_2.fastq.gz
ERR2675459_1.fastq.gz  ERR2675472_1.fastq.gz  ERR2675481_1.fastq.gz
ERR2675459_2.fastq.gz  ERR2675472_2.fastq.gz  ERR2675481_2.fastq.gz
ERR2675460_1.fastq.gz  ERR2675473_1.fastq.gz  ERR2675484_1.fastq.gz
ERR2675460_2.fastq.gz  ERR2675473_2.fastq.gz  ERR2675484_2.fastq.gz
ERR2675461_1.fastq.gz  ERR2675476_1.fastq.gz  ERR2675485_1.fastq.gz
ERR2675461_2.fastq.gz  ERR2675476_2.fastq.gz  ERR2675485_2.fastq.gz
ERR2675464_1.fastq.gz  ERR2675477_1.fastq.gz
ERR2675464_2.fastq.gz  ERR2675477_2.fastq.gz
```

### Clinical information

The clinical data has been simplified based on the information provided in [E-MTAB-6951](https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-6951). Download the `clinical.txt` file and place in the `/home/USER/SSAPs` folder

{% file src="/files/-M5WtwxyoN5jPTeu9FCi" %}
clinical.txt
{% endfile %}

{% code title="clinical.txt" %}

```bash
ENA_RUN	individual	age	sex	disease	sampling_site	paris_classification	microscopic_appearance	clinical_information	number_of_lesions	braf_status	kras_status
ERR2675454	S1	88	female	Colon Sessile Serrated Adenoma/Polyp	pre-lesion	0-IIa	SSA/P	no dysplasia	2	BRAF mutation c.1799T>A (V600E)	wild type KRAS
ERR2675455	S1	88	female	Colon Sessile Serrated Adenoma/Polyp	normal tissue adjacent to pre-lesion	normal	normal	none	NA	normal	normal
ERR2675458	S11	57	male	Colon Sessile Serrated Adenoma/Polyp	pre-lesion	0-IIa	SSA/P	no dysplasia	2	wild type BRAF	KRAS mutation c.37G>C (G13R)
ERR2675459	S11	57	male	Colon Sessile Serrated Adenoma/Polyp	normal tissue adjacent to pre-lesion	normal	normal	none	NA	normal	normal
ERR2675460	S12	49	male	Colon Sessile Serrated Adenoma/Polyp	pre-lesion	0-IIa	SSA/P	no dysplasia	3	BRAF mutation c.1799T>A (V600E)	wild type KRAS
ERR2675461	S12	49	male	Colon Sessile Serrated Adenoma/Polyp	normal tissue adjacent to pre-lesion	normal	normal	none	NA	normal	normal
ERR2675464	S15	36	female	Colon Sessile Serrated Adenoma/Polyp	pre-lesion	0-IIa	SSA/P	no dysplasia	2	BRAF mutation c.1799T>A (V600E)	wild type KRAS
ERR2675465	S15	36	female	Colon Sessile Serrated Adenoma/Polyp	normal tissue adjacent to pre-lesion	normal	normal	none	NA	normal	normal
ERR2675468	S17	53	female	Colon Sessile Serrated Adenoma/Polyp	pre-lesion	0-IIa	SSA/P	no dysplasia	1	BRAF mutation c.1799T>A (V600E)	wild type KRAS
```

{% endcode %}