Forum:Are there any workshops which are tailored to non-beginners/intermediate bioinformatics?

Question

[Daniel]

I've been in bioinformatics around 5 years, I'm comfortable on the command line, can QC NGS data, produce reasonable genomes and transcriptomes, and can generally achieve most of what I conceive in perl/python/R.

Are there any workshops that can help build on my experience? I'm thinking of things like appropriate assessing and improving the quality of assemblies, breaking down the hundreds of parts of the Tuxedo packages, traversing large datasets with things like bioconductor, bedops/tools...

Everything I seem to see advertised is aimed at beginners (which is definitely in requirement), but I'm looking to improve my skills and there are some things that you can only get from demonstrations, rather than reading manuals and --help pages.

Thanks

[Gjain]

Exactly what I am looking for...

[Daniel]

Thanks, I knew I couldn't be the only one!

[dariober]

I surmise (gut feeling opinion, please object) that there are not many courses out there at past-beginner level because a) the demand is lower b) not many people know what the advance level should be. I'm thinking especially about less mainstream analyses like ChIP-Seq, methylation, open chromatin mapping (as opposed to RNA-Seq, SNP calling). There is still a lot of debate about how these data should be best analyzed.

[alolex]

Yes! I have been looking for this too. Are any of these workshops for more advanced bioinformatics posted online anywhere? Most of what I find is for beginners.

Answer 1

[David Langenberger]

If you organize a group of people, we can also offer on-site courses. You can decide the topic, the length and the level and we organize the experts that will train you.

Check out http://www.ecseq.com/workshops/on-site-courses or http://www.ecseq.com/workshops/flyer/On-Site_Courses.pdf

[Daniel]

This is very interesting, thank you. Is there a min/max group size, and is it a fixed price regardless of number of attendees (within reason)?

[David Langenberger]

Dear Daniel,

there are no limits to the group size, but based on experience, we recommend groups smaller than 25 people. We also already performed one-to-one trainings for some big Pharma companies. The prices gradually decrease with more people. But, since we are talking about hands-on trainings, at some number we need more assistants/trainers. Overall, the prices depend on the size of the group, the number of days, the number of trainers/assistants needed, if the customer wants workshop modules that are already prepared, or if we have to design a new one, if the customer wants to use his/her own machines, if the customer wants to analyze his/her own data and many other things. We are very open to all possible compositions. If you are interested, we will have a call, discuss the agenda and then we will provide a quote.

Keep in mind that the complete group safes travel expenses, as well as arrival/departure days.

Note:

• All exercises in the courses will be performed with the most prominent open-source tools (e.g. bwa, Tuxedo Suite, DEseq, etc.) which can be used freely for later analysis. No commercial software is used!
• The course will be done using a bootable USB stick containing a Linux environment with all needed NGS tools already installed! After the course everyone will get the stick with all exercises and results created during the course to immediately apply the learned tasks with own data by just booting any machine (Windows, Mac, etc.) from the stick!

[Daniel]

Thank you again. I'm not in a position myself to book anything, but I can take this information to my supervisors and see if they would be interested in something like this, as I know there are plenty of people in the department that are in the same boat as me.

[Gjain]

That is great David. I see many workshops from you guys which looks awesome for beginners.

Something that I am interested are related to understand of algorithms related to NGS analysis, understanding of statistical concepts like normalization, significance testing etc. specific to various tools and packages commonly used in data analysis.

Also if possible to have some python oriented workshops too.

This is just an idea.

[David Langenberger]

We absolutely offer everything that you mentioned! You can decide what you want and then we will put together a package for you.

In public courses, you will always have to make a trade-off, otherwise you cannot do it in one week. Our philosophy is to offer only one topic, but in a way that everyone can follow. I, personally, don't like courses that claim to train you in one week in assembly, variant calling, diff. gene expression, gene/isoform prediction, methylation calling, peak calling (ChIP-Seq) and and and... that is not possible in one week. Researchers worked years on getting the knowledge in one of these fields, so how could they train others in one week? These courses are mostly just presentations where researchers show their pipeline... not more and not less. We try to use for every step different tools (mapping, quantification, diff. gene expression, etc.) and then the participant can think about which tool fits best for his/her task. That can be done for one topic in one very intense week.

Answer 2

[David Langenberger]

Dear Daniel,

there will be an RNA-Seq workshop in February next year. The first half might be not so interesting for you, but the second half is about RNA-Seq downstream stuff and pretty intense. Tuxedo will be compared with other tools, the different parameter settings and their effects will be discussed and non-standard transcripts (circularized RNAs and fusion genes) will be handled. I think it would fit your needs. But, we can only offer it together with a short introduction to Linux and NGS... but participants with expertise, like you, told us, that is still interesting and they learned some new stuff. We will show pretty cool linux tricks, explain illumina biases and error sources and compare four different mapping tools.

Check our the course's website if you are interested.

There will also be an assembly course directly after the RNA-Seq course. It will be online soon. We found an expert in genome and transcriptome assembly and he will spend 3 days to explain the different assembly methods and then compare different tools and train you in understanding and optimizing the results. Since he is doing assemblies for pretty big international projects, he really knows what he is talking about. Check our website in one or two weeks, then the course will show up. You can also sign up for our newsletter (at the bottom of the main page) and we'll let you know, once it is online.

Cheers,
David

[David Langenberger]

One add: Both courses will be hands-on practical courses - You will analyze the data yourself!

Answer 3

[Emily]

There's an Advanced ChIP-seq and RNA-seq analysis course at the EBI in April. Generally EBI courses are topic focussed, rather than level focussed, so they're worth attending if you're interested in a particular topic, even if the early parts of the courses might be a tad simple for you.