How to run HTseq on the public galaxy platform?

Question: How to run HTseq on the public galaxy platform?

4.6 years ago by

Hi all,

I'm trying to run the HTseq function using the data I generated on the public Galaxy platform. However, apparently there's no built-in HTseq function in the platform. Is there a way to generate data on the platform? Or I have to download all my data and run it otherwhere?

Thank you!

Nancy

rna-seq galaxy htseq • 3.3k views

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modified 2.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.6 years ago by Yanxiang Shi • 20

2.6 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

You can find the tool htseq_count at http://usegalaxy.org under the tool group NGS: RNA Analysis. It has been there for several months.

Thanks, Jen, Galaxy team

ADD COMMENT • link written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k

4.6 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

There is only one HTseq function wrapped for Galaxy so far, but keep watching the Tool Shed, since the paper just went out (late Feb 2014). It is for use is a local/cloud Galaxy (not Main - usegalaxy.org).

To locate in the Tool Shed http://usegalaxy.org/toolshed:

Repository 'htseq_count'
Synopsis: Count aligned reads (SAM/BAM) that overlap genomic features (GFF)

I did not check the other public Galaxy servers, but these do change content frequently, so a review may be worth it: https://wiki.galaxyproject.org/PublicGalaxyServers. Or maybe someone running one, also running HT tool(s), will see the post and add to it!

If you are just looking for similar functions, comparing interval regions is one of the things that Galaxy does best. Look in the tool group "Operate on Genomic Intervals" and "BED Tools" for options. Nearly any file can be converted to interval format, although some of these tools work with other formats directly. If you have a specific operation/goal in mind, please ask.

Best, Jen, Galaxy team

ADD COMMENT • link modified 4.6 years ago • written 4.6 years ago by Jennifer Hillman Jackson ♦ 25k

Hi,

are you planning on putting htseq-count on usegalaxy, I think it is a great tool and lot of people will be happy to see it?

ADD REPLY • link written 3.3 years ago by vebaev • 130

No progress in 23 months =(.

ADD REPLY • link written 2.6 years ago by alexander.lenail • 0

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