Fill the hands-on tutorial and the slides for main ChIP-seq tutorial and add a Galaxy tour

[bebatut]

Hi,

I started to fill the tutorial and the associated slides for ChIP-seq with previous tutorial content.

We need to end to fill it with previous tutorial content by formatting the content to new templates. We can also take inspiration from:

• https://drive.google.com/file/d/0B9urRnOAUUI8UmwzbTVpdmZucWM/view
• https://drive.google.com/file/d/0B9urRnOAUUI8cHpzYVBscjNKWEE/view

We also need to add a Galaxy tour

Thanks,

Bérénice

[malloryfreeberg]

Hi @bebatut!

I and my colleague @moheydarian are interested in contributing to tutorial content, including a ChIP-seq analysis tutorial. We have a curated set of published ChIP-seq data, workflows, etc. that have worked well for past training sessions. Would it be alright to format our content to the new templates? Or would it be preferred to keep the current ChIP-seq training data?

Either way, we are excited to contribute :)

[friedue]

Hi Mallory, just curious: what data do you use? Does it cover a range of QC/peak types etc.? The initial ChIP-seq training set is pretty old and shallowly sequenced, so updated material may not be a bad idea.

[bgruening]

@malloryfreeberg both should work. We are currently not sure how to handle multiple tutorials. I hope we can merge as many things we can and have one really good tutorial. But if we have two separated ones this is also good - in this case it is key to communicate to our users which tutorial does what, what are the difference and when do we recommend the one or the other. Does this makes sense?

We will also move the slides to pure markdown soon, so don't spend time in creating the reveal.js slides, we will auto generate those. More about this will follow soon.

Great to have you on board @malloryfreeberg! Greetings to Mo!

[malloryfreeberg]

Hi @friedue,

We are using Tal1 ChIP-seq data (with replicates and input controls) from GSE51338 in GEO. There is also corresponding RNA-seq data in this study that we would like to incorporate somehow. We have downsampled the ChIP-seq data to include a subset of interesting loci identified in the associated paper.

@bgruening, we can certainly work on creating tutorial material with both the previous ChIP-seq data and this updated data, and then later decide if having both tutorial is worthwhile.

[friedue]

@malloryfreeberg do you have your current tutorial online somewhere? sounds like a good data set (i.e., often used model organism, solid data, good results)

[malloryfreeberg]

@friedue not yet. @moheydarian and I were going to create a Galaxy Page tutorial today, and then came across all the training materials here. So, rather than just create a Page (which we still want to do), we thought we could directly contribute to this repo.

[friedue]

do you use deepTools, too? I see you're in Baltimore - I'm up in New York, we could also have a telephone chat if that's quicker than an online discussion (and if that's ok with @bebatut - I've just taken the liberty here because most of the links point to material I've set up or contributed to) btw, the link to the previous tutorial is broken @bebatut

[MoHeydarian]

Hi @friedue, We haven't incorporated deepTools in our version of the chIPseq exercise, yet and are open to doing so. Is there a feature of deepTools you would like to see incorporated?

A telephone chat is fine, but I would vote for keeping this discussion thread online so others can follow and contribute.

[bgruening]

@MoHeydarian all? ;) Seriously, the QC and heatmap plotting is unmatched imho and is every time a wow effect during workshops.

[bebatut]

Hi all,

@malloryfreeberg Welcome aboard. Thanks!

As @bgruening mentioned, things will change (a bit) soon (before the end of the week, I hope). Everything will be based on markdown (tutorials and slides). I will keep in touch to explain you the changes :)

@friedue I will fix the broken links during the changes.

Thanks again

[friedue]

absolutely, I would leave this thread open.

deepTools has numerous features that are particularly helpful for ChIP-seq, most importantly QC (correlation, coverage, enrichment) and normalization (for sequencing depth, vs. input) as Bjoern mentioned they also have a useful visualization features. any time you'd prefer for a phone call today, @malloryfreeberg @MoHeydarian?

so many kudos for basing everything on markdown, @bebatut and @bgruening!!

[MoHeydarian]

Anytime this afternoon works for us, @friedue. Lets do a public Google hangout so others can join if they like (link: https://hangouts.google.com/call/kjpev2h7b5h5ho2a7xjrhu3ro4e) and lets aim to chat sooner than later in case our friends in other timezones would like to join.

[friedue]

2pm EST?

[MoHeydarian]

Sounds good for @malloryfreeberg and I. Talk soon.

[bgruening]

I need to leave soon, sorry will not be able to join! Enjoy and rock the training world!

[friedue]

stuck in a presentation, will be 10 min late

[friedue]

nice chat yesterday! to get a feeling for how we typically use deepTools for ChIP-seq, you can check out this page

we also have a couple of step-by-step protocols

[malloryfreeberg]

Thanks for the chat, @friedue! We've implemented some deepTools functions in our workflow, but we are observing a strange trend in the plotFingerprint graph. Perhaps we can share our history/workflow with you today and get some feedback (on plotFingerprint or anything else)?

[friedue]

yes, totally. frd2007 at med dot cornell dot edu

[malloryfreeberg]

@friedue is that your Galaxy Main username? I can't find you to share the workflow :(

[friedue]

galaxy user name is friedue, but do send me an email for the back and forth about the workflow that's probably going to follow (slack's fine, too; same email address)

[malloryfreeberg]

Hey @bgruening, can you make a new branch under "training-material" called "chip-seq-tutorial-mfreeberg" or something similar, so that I can create a PR with which to merge mine and Mo's updated ChIP-seq tutorial branch? At least, I think this is how this is supposed to work... Thanks!

[bgruening]

@malloryfreeberg how about I add you all to this repo? :)

[bgruening]

Done! :) Thanks so much for contributing!

[bebatut]

We now have 2 tutorials for ChIP-seq we can work on: http://galaxyproject.github.io/training-material/topics/chip-seq/