Bulk RNA-seq data workshop improvements

[ayushi-agrawal-gladstone]

[ ] Add a slide on publicly available data, how to access it and how to clean it up (maybe share a script for clean up?)

[ayushi-agrawal-gladstone]

Updating list based on questions during the workshop:

• Add a slide on publicly available data, how to access it and how to clean it up (maybe share a script for clean up?)
• How do multiple input fastq files fit into the pipeline? (specify during the demo)
• Cutadapt paper mentions a case where the adapter is in the middle of the read like: ATCTGGGGapaterATG. When would such a read arise?

[ayushi-agrawal-gladstone]

Updating list based on questions during the workshop:

• Add a slide on publicly available data, how to access it and how to clean it up (maybe share a script for clean up?)
• How do multiple input fastq files fit into the pipeline? (specify during the demo)
• Cutadapt paper mentions a case where the adapter is in the middle of the read like: ATCTGGGGapaterATG. When would such a read arise? Add a better visual from their manual.
• Fix error the pseudo-alignment slide - it should say these tools align to transcriptome and not to genome.

[ayushi-agrawal-gladstone]

In the workshop held on August 19-20, 2024, there were a lot of Docker issues encountered by the participants irrespective of the OS they used.

Issues:

• Some participants had university provided laptops where there were security firewalls that prevented them from downloading Docker Desktop or caused issues while pulling the docker image
• A lot of errors denying access to hub without login when pulling the docker image
• Docker desktop opened but gave "command not found" error when running docker --version on the terminal/command prompt.
• Docker desktop either crashed or froze when trying to run the container
• Due to bandwidth issues, terminal/command prompt got stuck when pulling the docker image
• Docker container is not mounting and got the following error: _assertion failed [result.value != EEXIST]: VmTracker attempted to allocate existing mapping (ThreadContextVm.cpp:47 mmap)_
• Latest docker version incompatible with some old OS versions (e.g. Mac OS BigSur). If older compatible versions were installed, then problems with image pulling or no access on terminal

Ideas for next workshop:

• Office hours before or after the workshop
• Make a slide with a list of things all registrants should ensure so that there are no issues with Docker.
• Have registrants run few steps as pre-workshop instructions so that if they have issues they can reach out before the workshop. For example, ask them to run up until pulling docker image.
• Can we run the nf-core pipeline during the demo? This will also be closer to what we actually do with real data in the core. Need to evaluate:
  - Is nextflow and nf-core available for windows, linux and mac? They do have installation instructions for all: https://nf-co.re/docs/usage/getting_started/installation
  - Can we use our own reference genome with nf-core rna-seq pipeline?
  - Can we run only one tool at a time with nf-core rna-seq pipeline?

@MichelaTr Please feel free to add if I missed something or if there are other ideas you might have. Thanks!