ATAC-seq analysis and tutorial

[Chiqui]

Hi there,

I’m following the tutorial for ATAC-seq analysis for the platform. They use Genrich for peak calling but it doesn’t show up when I look for it in “tools”. Isn’t it available yet?

Thanks!

[jennaj]

Welcome @Chiqui

Not all tools are available at all public Galaxy servers. Some are domain-specific. Some have unique tools. If running your own server, tools are usually in the ToolShed https://usegalaxy.org/toolshed and can be installed, but not always.

That is a lot of “sometimes”. So let’s break this down into smaller pieces and work on a solution from there. Specifically, these details would help:

1. What exact tutorial are you following? Link/URL?

2. Which Galaxy server are you currently working at? URL please if public. Describe the source/server type if not public (it is Ok if you don’t know the non-public full details, just share what you can).

Thanks!

[Chiqui]

Hi! Thanks for the reply!

1. I’m following this tutorial: https://galaxyproject.github.io/training-material/topics/epigenetics/tutorials/atac-seq/tutorial.html
2. I’m using the web-base platform (usegalaxy.org) so it seems it works with CyVerseat the Texas Advanced Computing Center

Is there any other way to work with Galaxy in a user-friendly manner that doesn’t depend on the website? I am not a bioinformacitian and even though I have some knowledge of R, it’s hard for me to analyze data using scripts. That’s why I was amazed when I found and started using the website.

Well, I hope you can help me!

Best!

[lldelisle]

Hi,
I am very happy to see that this tutorial is used.
When you go to the tutorial webpage, in the overview frame, you have an icon written Galaxies. If you click on it, you will see where you can run the full pipeline. As you will see, you can run it on usegalaxy.eu.

I hope it helps,

Best

[jennaj]

Thank you @lldelisle!!

You are definitely correct. Below is just a bit more help where I shared this same info in more generalized terms:

Troubleshooting resources for errors or unexpected results

Galaxy Training Network Tutorials: Some GTN tutorials are appropriate for Galaxy Main and some are not. Where you can run each is noted per tutorial – click on the Galaxy instances gear icon to review the Public Galaxy server choices. If a tutorial is supported by a pre-configured Galaxy Docker training image, instructions for how to get it will be listed below the tutorial listings, per category.

[Chiqui]

Thank you so much!!! Appreciate it! I haven’t noticed there were different Galaxies

[Chiqui]

Thanks!! Nothing will stop me now!

[Tini]

Hi, I have a question that maybe is stupid. But I used the indices suggested by Buenrostro´s protocol according to that what sequence should I take to perform the Cutadapt?

Thanks

[jennaj]

Welcome @Tini

How and if to trim adaptor depends on your fastq read data content.

Review your FastQC as shown in the tutorial – were any detected? You can post back a screenshot if you want.

[Tini]

Thanks this is what i got in the FastQC.

[jennaj]

This is the same adapter as in the tutorial, so you can use the same adaptor sequence and follow the instructions exactly.

[Tini]

thanks for your help, i would like to know do you know which sequences to use?, because i have other samples that look so similar to the photo i sent but then the cut adapt did not work.
I attached an example of other sample.

Thanks

[jennaj]

@Tini

You could try Trimmomatic instead. There is an option built-in to trim Nextera paired-end adaptors.