import pandas as pd
event_data_cached = pd.read_csv("https://docs.google.com/spreadsheets/d/e/2PACX-1vRqatWozaX_-OaBG_9Peoj4RknvI1OMUOpHUbb8TvzzN8aB5VFGLpLTlqrkY9iavuKZPl9eH0I3Aozm/pub?gid=0&single=true&output=csv")
ojs_define(event_data_cached = event_data_cached)

all_events = transpose(event_data_cached)
event = all_events.find(row => row.link?.trim() === 'news/2026-01-13-metatranscriptomics.html') ?? {}

Workshop

Metatranscriptomics

Hands-on online workshop designed for HPC beginners. Learn to analyse and visualise RNA-seq data using command line tools.

About the Workshop

We start by teaching the essential tools used in High Performance Computing such as file systems and the command-line to connect to and use cloud computing for file navigation and script writing. We then explore how to clean and prepare raw RNA-seq data through quality control and rRNA removal to enable detailed taxonomic and functional profiling of the microbial community. The process culminates in the visualisation of these insights using interactive tools like Krona to facilitate interpretation.

All the software and data used in the workshop are hosted on an Amazon Machine Image (AMI). We will give you details as to how to access these instances after registration.

What you will learn

• File systems and using the command line: How to log into and navigate an HPC system
• Quality control for metatransciptomcs: An introduction to metatranscriptomics and preprocessing with sortmeRNA
• Taxonomic profiling: Analysis of community taxonomy with Metaphlan
• Functional profiling: Analysis of community function with Humann

Programme

The course takes place over two weeks and combines teaching and live coding with time spent out of the zoom room while long analyses complete. There are drop-in sessions

Week 1
Monday, 11 May	10:00 - 12:00	File systems and directories
Tuesday, 12 May	10:00 - 12:00	Using the command line
Wednesday, 13 May	10:00 - 13:00	An introduction to metatranscriptomics, quality control and preprocessing
Thursday, 14 May	13:00 - 14:00	Online troubleshooting drop-in session (optional)
Friday, 15 May	10:00 - 11:30	Review of sortmeRNA. Taxonomic profiling of communities with Metaphlan.

Week 2
Monday, 18 May	13:00 - 14:00	Online troubleshooting drop-in session (optional)
Tuesday, 19 May	10:00 - 12:00	Functional profiling of communities with Humann
Wednesday, 20 May	14:00 - 15:00	Online troubleshooting drop-in session (optional)

Audience

This workshop is aimed at researchers with no prior experience of the tools covered in the workshop. However, participants will need some familiarity with biological concepts such as genomes and microbiomes.

Prerequisites

To participate in this course, you will need a computer with internet access. The software and data used for analysis during the course are hosted on an Amazon Web Services (AWS) virtual machine (VM) instance.

To access your AWS instance from your personal computer, you will need a shell or terminal. This shell is available by default for Linux and Mac users but Windows users will need to install Git for Windows.
Detailed Pre-course instructions

html`
<h3>Event Details</h3>

<div class="event-detail-item">
  <div class="event-detail-icon">
    <i class="fa-regular fa-calendar-days"></i>
  </div>
  <div class="event-detail-content">
    <p>Date</p>
    <p>${event.date || 'TBA'}</p>
  </div>
</div>

<div class="event-detail-item">
  <div class="event-detail-icon">
    <i class="fa-regular fa-clock"></i>
  </div>
  <div class="event-detail-content">
    <p>Time</p>
    <p>${event.time || 'TBA'}</p>
  </div>
</div>

<div class="event-detail-item">
  <div class="event-detail-icon">
    <i class="fa-solid fa-location-dot"></i>
  </div>
  <div class="event-detail-content">
    <p>Location</p>
    <p>${event.location || 'Online'}</p>
  </div>
</div>

<div class="event-detail-item">
  <div class="event-detail-icon">
    <i class="fa-solid fa-sterling-sign"></i>
  </div>
  <div class="event-detail-content">
    <p>Fees</p>
    ${(event.fees || '').split('\n').map(line => `<p>${line}</p>`).join('')}
  </div>
</div>

<a href="${event.register_link || '#'}" class="register-button">Register Now</a>

<p class="event-note">Limited to 30 places</p>

<div class="questions-section">
  <p>Questions?</p>
  <a href="mailto:research-digital-skills@york.ac.uk">research-digital-skills@york.ac.uk</a>
</div>
`