Forum:Wanted: Analysis of RNA-seq data with Bioconductor short course/training (~3 months)

Question

[bioinfo17]

special interests in Deseq2, gene enrichment and pathway analysis etc. Any suggestions please anyone? Most of the tutorials available are based on model organisms. Was wondering if there are any courses available - not looking for short courses, proper 3 months training?

[WouterDeCoster]

Most of the tutorials available are based on model organisms.

And that's not what you are looking for?

[bioinfo17]

Yes that's correct, not looking for courses based on model organisms.

[Michael]

I changed this request to Forum. Your request is lacking information, e.g. where you are located, I guess you want a local course? Are you sure you need 'proper 3 months' training? Possibly start with a short course, then check how to move on? A lot of courses are announced here. Check the Similar posts on the right, or check with your university or local R-user group.

[bioinfo17]

Have attended short courses previously but was of little help, was great for understanding the basics but again all available courses or tutorials offered use model organisms. In talks with local R-users but no luck yet! I am indeed looking for a proper training course specifically Deseq2 and post RNA-seq analysis steps such as gene enrichment and pathway analysis etc as mentioned above. It doesn't necessarily have to be three months but would be good if the courses are detailed (maybe weeks and not days) - thanks

[GenoMax]

It is a supply and demand scenario. It takes time/effort to create course materials and unless there is enough demand it would be hard to justify the expense of creating a course for an uncommon experimental organism.

You have also not said if you would be willing to pay for such a course. Not many are.

You should be able to acquire of basics of analysis no matter what the underlying material being used for the course. As for the rest you are going to be at the mercy of the information available for your non-model organism (as noted by @Michael in his answer).

Answer 1

[Michael]

As you are referring specifically to non-model organisms, and we are working with one, let me share my experiences.

There are several shortcomings with NMOD's that possibly contribute to the fact that most courses will focus on MOD's. In principle, the analysis is more complex and also variable in many respects.

• NMOD's have more fragmented and lower quality genome sequences, if at all, or you have to use or even assemble a transcriptome
• these are normally not as well annotated
• harder to get good data
• there is possibly no 'official' gene build, identifiers, and functional annotation (GO, Kegg, gene names)
• you can generate such predictions in several ways but all will be predicted only, 'IEA' (inferred by electronic annotation, for GO terms for example, which some also recommend to filter out). These annotations will be considered unreliable by many.
• a lot of higher level tools do not support the DIY annotations and NMOD's (that limits the choice at this step)

The items mentioned above possibly do not help to build a clean and easy course curriculum, because you needed to cover the whole work-flow to fill in the gaps mentioned above to get started, almost starting with the assembly, or omit some parts which could be essential to other organisms. For further complication, not all of these tasks belong in Bioconductor either.

However, I think it should be possible to build such a curriculum into a 2-3 week course, with information gathered from different sources, e.g. the BioStars handbook (not sure how much it covers for NMOD's), some questions from the forums and the available documentation. Or one could work this out in self-study.

[Michael]

If you want to consider an internship with us this year, maybe we can figure something out. Or you could of course try another institute. Check http://www.slrc.no/

[bioinfo17]

That's great, thanks :)