# Almost Everything about ChIP-Seq data analysis. Focus on a beginner

**URL:** <https://help.galaxyproject.org/t/almost-everything-about-chip-seq-data-analysis-focus-on-a-beginner/1546>\
**Category:** usegalaxy.org support\
**Tags:** macs2, chip-seq, mapping, epigenetics, quality-control\
**Created:** [June 14, 2019, 10:51am UTC](https://help.galaxyproject.org/t/almost-everything-about-chip-seq-data-analysis-focus-on-a-beginner/1546 "2019-06-14T10:51:04Z")\
**Posts on this page:** 1\
**Showing post:** 11

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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [June 20, 2019, 7:43pm UTC](https://help.galaxyproject.org/t/almost-everything-about-chip-seq-data-analysis-focus-on-a-beginner/1546/11 "2019-06-20T19:43:17Z")

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> [@1113](#):
>
> **RECOMMENDATION for galaxy:** I wish Galaxy has some indicator of how much computationally demanding a job could be (and how much data it would produce - to estimate if a user goes over their quota).

This is almost impossible to predict, for reasons I already stated:

> [@jennaj](#):
>
> Actual execution time for a job (once the job turns yellow) can vary widely based on your input size/content, the parameters used, and how that tool normally runs (outside of Galaxy).

> [@1113](#):
>
> Q1. I thought to temporarily remove datasets from my Galaxy (main) account, but downloading takes ages. I do data upload via FTP and that works faster. Is there a way to download data from Galaxy faster?

Try using `wget` or `curl` to download larger datasets. FAQ: [Downloading Data](https://galaxyproject.org/support/download-data/)

> [@1113](#):
>
> Q2. Looking for the solutions for my “space” problem I read this  
> [Galaxy CloudMan - Galaxy Community Hub](https://galaxyproject.org/cloudman/)  
> I guess running a cloud cluster is not something for users with 1 project only.

Actually, many scientists use Cloudman/AWS for all sorts of reasons, including personal use when their needs are more than the public server can supply. It has much pre-configured, resource allocation is flexible, and you’ll be the admin so can add in (or remove) tools as you want. If costs are a concern, AWS offers grants for research work. Most of the configuration is web-based, except for some of the initial steps involved when setting up an AWS account. We have detailed FAQs to help with that part, as does AWS.

FAQs & links:

- [Galaxy Choices - Galaxy Community Hub](https://galaxyproject.org/choices/)
- [Galaxy Platform Directory: Servers, Clouds, and Deployable Resources - Galaxy Community Hub](https://galaxyproject.org/use/)
  - [Amazon Web Services (AWS) - Galaxy Community Hub](https://galaxyproject.org/use/aws/)
  - [Galaxy and the Cloud - Galaxy Community Hub](https://galaxyproject.org/cloud/)
  - [AWS Programs for Research and Education](https://aws.amazon.com/grants/)

- This area is for teaching but includes advice about what types of resources to allocate – even if just using a cloud version of Galaxy for your own work: [Galaxy Community Hub - Galaxy Community Hub](https://galaxyproject.org/teach/)
- The broader Galaxy Ecosystem overview for reference: [https://galaxyproject.github.io/](https://galaxyproject.github.io/)

To manage your account quota space at any Galaxy server (in particular, public Galaxy servers), be aware that you need to _permanently delete (purge)_ data to have it not count toward quota. _Deleting_ is not enough. FAQ: [Checking for active vs deleted vs permanently deleted (purged) datasets and histories](https://galaxyproject.org/learn/managing-datasets/#delete-vs-delete-permanently)

It seems like a lot of your questions have already come up or have existing FAQs/tutorials. The post I sent before ([Troubleshooting resources for errors or unexpected results](https://help.galaxyproject.org/t/troubleshooting-resources-for-errors-or-unexpected-results/42)) has much of this type of help information consolidated in one place. You can also search prior Q&A and all other Galaxy resources directly: [Galaxy Support - Galaxy Community Hub](https://galaxyproject.org/support/#help-resources) \>\> the first option points to here: [Galaxy Community Hub - Galaxy Community Hub](https://galaxyproject.org/search/)

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