# Work environment

## Environment

* CPU: Intel® Xeon® E5-2623 v3 (Quad-Core; 8 Threads)
* Memory: 64 GB
* Ubuntu 18.04.4 LTS
* R version 3.6.2 (2019-12-12)

{% hint style="info" %}
CPU usage is limited to 6 threads and memory to 32 GB where applicable
{% endhint %}

## Directories

| Path                           | Purpose                                                      |
| ------------------------------ | ------------------------------------------------------------ |
| `/home/USER/tools`             | Software/tools                                               |
| `/home/USER/db/refanno`        | Reference genome, annotation and index                       |
| `/home/USER/SSAPs`             | RNA-seq exercise on sessile serrated adenomas/polyps dataset |
| `/home/USER/SSAPs/fastqs`      | FASTQ files                                                  |
| `/home/USER/SSAPs/trimmed`     | Trimmed FASTQ files                                          |
| `/home/USER/SSAPs/salmon`      | Output from Salmon                                           |
| `/home/USER/SSAPs/star`        | Output from STAR                                             |
| `/home/USER/SSAPs/salmon_star` | Output from STAR+Salmon                                      |
| `/home/USER/SSAPs/rsem_star`   | Output from STAR+RSEM                                        |
| `/home/USER/SSAPs/analysis`    | R analysis (DGE, DTE, and DTU)                               |

